CompaRNA - on-line benchmarks of RNA structure prediction methods

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All RNAs from the PDB dataset
extended base pair definition

	All RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. The "extended" secondary structure definition includes all interacting bases using Watson-Crick, Hoogsteen or sugar edges, in both cis and trans orientations, including also base pairs conforming to the "standard" definition (the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry). Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: June 16, 2013
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Number of RNA sequences: 153
Robustness test: no

Important! This ranking will be updated in future, when predictions for new RNAs are generated by the methods being tested. This ranking shows the performance of methods as of June 16, 2013.

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 23) of the comparisons were based on at least 10 predictions for common targets).

The ratio 40% / 60% was chosen in order not to bias methods for which not enough predictions have been collected.

Summary of pairwise comparisons

58 methods predicting RNA secondary structure were compared with each other (thus each method has 57 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 34 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Tested since	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	CentroidAlifold(20)	yes	2009-07-01	49	1	0	7	40	39
2	PETfold_pre2.0(seed)	no	2011-11-03	46	0	0	11	27	27
3	ContextFold	yes	2011-11-15	42	4	1	10	62	61
4	MXScarna(seed)	no	2009-06-15	42	6	1	8	63	61
5	RNAalifold(20)	no	2009-02-18	39	6	1	11	42	41
6	PPfold(20)	yes	2011-04-18	38	2	1	16	23	21
6	PETfold_pre2.0(20)	no	2011-11-03	38	2	1	16	19	19
8	IPknot	yes	2011-07-01	37	11	1	8	70	69
9	CentroidAlifold(seed)	yes	2009-07-01	37	12	2	6	62	61
10	RNASampler(20)	no	2009-02-18	36	9	1	11	42	41
11	TurboFold(20)	no	2011-04-20	35	5	1	16	23	21
12	MXScarna(20)	no	2009-02-18	35	9	2	11	42	41
13	Sfold	no	2009-02-18	34	16	0	7	153	152
14	CentroidHomfold‑LAST	yes	2011-05-11	31	14	4	8	77	67
15	Contrafold	yes	2009-02-18	31	16	3	7	153	152
16	RNAalifold(seed)	no	2009-02-18	30	10	3	14	64	38
17	HotKnots	no	2009-02-18	29	19	2	7	153	147
18	MaxExpect	yes	2009-10-15	29	20	1	7	132	130
19	CentroidFold	yes	2009-08-01	29	22	1	5	138	137
20	UNAFold	no	2009-02-18	26	20	4	7	153	152
20	PknotsRG	no	2009-02-18	26	20	4	7	153	151
22	ProbKnot	yes	2010-08-10	26	23	1	7	106	105
23	Murlet(20)	yes	2009-02-18	24	18	4	11	42	41
24	RNAfold	no	2009-02-18	24	23	3	7	153	152
25	Carnac(20)	no	2009-02-18	23	20	3	11	42	41
26	RNAshapes	no	2009-02-18	23	26	1	7	153	147
27	Fold	no	2010-03-15	22	25	3	7	114	113
28	TurboFold(seed)	no	2011-04-20	20	6	4	27	31	15
29	RSpredict(20)	no	2009-06-03	20	26	4	7	41	40
30	Afold	no	2009-02-18	19	21	3	14	153	109
31	RNAsubopt	no	2009-02-18	19	29	2	7	153	147
32	RNASLOpt	no	2011-11-01	16	29	1	11	62	59
33	Cylofold	no	2010-06-08	16	28	3	10	108	77
34	McQFold	yes	2009-02-18	16	32	2	7	153	151
35	Multilign(20)	no	2011-03-01	14	27	0	16	24	21
36	CRWrnafold	yes	2011-08-23	13	11	3	30	68	32
37	Pknots	no	2009-02-18	13	36	1	7	153	142
38	RNASampler(seed)	no	2009-02-18	12	14	3	28	64	22
39	Alterna	no	2009-02-18	12	29	1	15	153	89
40	Mastr(20)	yes	2009-02-18	12	34	0	11	42	41
41	Vsfold4	no	2009-02-18	10	39	0	8	153	140
42	Murlet(seed)	yes	2009-02-18	9	32	1	15	64	34
43	Vsfold5	no	2009-02-18	6	41	3	7	153	138
44	MCFold	yes	2009-02-18	6	44	1	6	153	131
45	RDfolder	no	2009-02-18	5	39	0	13	153	99
46	RNAwolf	yes	2011-07-01	5	44	2	6	70	69
47	NanoFolder	yes	2011-11-17	4	31	0	22	52	36
48	PPfold(seed)	yes	2011-04-18	2	43	1	11	31	27
49	RSpredict(seed)	no	2009-06-03	2	48	1	6	63	62
50	Carnac(seed)	no	2009-02-18	1	46	0	10	64	39
51	Mastr(seed)	yes	2009-02-18	1	48	0	8	64	62
N/A	CMfinder(20)	yes	2012-09-01	4	4	1	48	14	11
N/A	Multilign(seed)	no	2011-03-01	3	1	0	53	32	11
N/A	CMfinder(seed)	yes	2012-09-01	0	0	0	57	19	0
N/A	DAFS(seed)	yes	2012-11-20	0	0	0	57	17	0
N/A	DAFS(20)	yes	2012-11-20	0	0	0	57	13	0
N/A	PETfold_2.0(seed)	no	2013-05-20	0	0	0	57	2	2
N/A	PETfold_2.0(20)	no	2013-05-20	0	0	0	57	1	1

Detailed results of pairwise comparisons between methods

Legend:

+	method on the left scored higher in this pairwise comparison
-	method on the left scored lower in this pairwise comparison
=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)

P-values were obtained using Wilcoxon signed-rank test taking 2 sets of 40 MCC values obtained for 40 random subsets of 90% of the dataset for each pair of methods. If the P-value is lower than 0.001 and there are at least 10 sequences on which benchmark was performed, the difference between the performance of two methods is assumed to be statistically sound.


CentroidAlifold(20)		- PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 CentroidAlifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.597 CentroidAlifold(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.870 CentroidAlifold(20): 0.864 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.656 ContextFold: 0.617 Sensitivity CentroidAlifold(20): 0.501 ContextFold: 0.499 Positive Predictive Value CentroidAlifold(20): 0.864 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.669 MXScarna(seed): 0.642 Sensitivity CentroidAlifold(20): 0.513 MXScarna(seed): 0.528 Positive Predictive Value CentroidAlifold(20): 0.877 MXScarna(seed): 0.784 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAalifold(20): 0.646 Sensitivity CentroidAlifold(20): 0.516 RNAalifold(20): 0.499 Positive Predictive Value CentroidAlifold(20): 0.879 RNAalifold(20): 0.838 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.656 PETfold_pre2.0(20): 0.649 Sensitivity CentroidAlifold(20): 0.501 PETfold_pre2.0(20): 0.530 Positive Predictive Value CentroidAlifold(20): 0.864 PETfold_pre2.0(20): 0.798 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64089763604e-07	+ CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.668 PPfold(20): 0.662 Sensitivity CentroidAlifold(20): 0.515 PPfold(20): 0.526 Positive Predictive Value CentroidAlifold(20): 0.870 PPfold(20): 0.837 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.669 IPknot: 0.526 Sensitivity CentroidAlifold(20): 0.511 IPknot: 0.433 Positive Predictive Value CentroidAlifold(20): 0.880 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 CentroidAlifold(seed): 0.589 Sensitivity CentroidAlifold(20): 0.516 CentroidAlifold(seed): 0.379 Positive Predictive Value CentroidAlifold(20): 0.879 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNASampler(20): 0.609 Sensitivity CentroidAlifold(20): 0.516 RNASampler(20): 0.466 Positive Predictive Value CentroidAlifold(20): 0.879 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.668 TurboFold(20): 0.625 Sensitivity CentroidAlifold(20): 0.515 TurboFold(20): 0.518 Positive Predictive Value CentroidAlifold(20): 0.870 TurboFold(20): 0.759 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 MXScarna(20): 0.617 Sensitivity CentroidAlifold(20): 0.516 MXScarna(20): 0.514 Positive Predictive Value CentroidAlifold(20): 0.879 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Sfold: 0.558 Sensitivity CentroidAlifold(20): 0.516 Sfold: 0.468 Positive Predictive Value CentroidAlifold(20): 0.879 Sfold: 0.669 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.683 CentroidHomfold‑LAST: 0.594 Sensitivity CentroidAlifold(20): 0.533 CentroidHomfold‑LAST: 0.501 Positive Predictive Value CentroidAlifold(20): 0.880 CentroidHomfold‑LAST: 0.709 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Contrafold: 0.534 Sensitivity CentroidAlifold(20): 0.516 Contrafold: 0.474 Positive Predictive Value CentroidAlifold(20): 0.879 Contrafold: 0.607 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.601 RNAalifold(seed): 0.557 Sensitivity CentroidAlifold(20): 0.416 RNAalifold(seed): 0.334 Positive Predictive Value CentroidAlifold(20): 0.871 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.673 HotKnots: 0.532 Sensitivity CentroidAlifold(20): 0.516 HotKnots: 0.477 Positive Predictive Value CentroidAlifold(20): 0.879 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.673 MaxExpect: 0.553 Sensitivity CentroidAlifold(20): 0.516 MaxExpect: 0.480 Positive Predictive Value CentroidAlifold(20): 0.879 MaxExpect: 0.641 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 CentroidFold: 0.537 Sensitivity CentroidAlifold(20): 0.516 CentroidFold: 0.456 Positive Predictive Value CentroidAlifold(20): 0.879 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 UNAFold: 0.541 Sensitivity CentroidAlifold(20): 0.516 UNAFold: 0.477 Positive Predictive Value CentroidAlifold(20): 0.879 UNAFold: 0.619 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.673 PknotsRG: 0.554 Sensitivity CentroidAlifold(20): 0.516 PknotsRG: 0.495 Positive Predictive Value CentroidAlifold(20): 0.879 PknotsRG: 0.626 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.666 ProbKnot: 0.545 Sensitivity CentroidAlifold(20): 0.504 ProbKnot: 0.484 Positive Predictive Value CentroidAlifold(20): 0.883 ProbKnot: 0.619 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Murlet(20): 0.582 Sensitivity CentroidAlifold(20): 0.516 Murlet(20): 0.430 Positive Predictive Value CentroidAlifold(20): 0.879 Murlet(20): 0.793 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAfold: 0.538 Sensitivity CentroidAlifold(20): 0.516 RNAfold: 0.480 Positive Predictive Value CentroidAlifold(20): 0.879 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Carnac(20): 0.579 Sensitivity CentroidAlifold(20): 0.516 Carnac(20): 0.374 Positive Predictive Value CentroidAlifold(20): 0.879 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAshapes: 0.536 Sensitivity CentroidAlifold(20): 0.516 RNAshapes: 0.473 Positive Predictive Value CentroidAlifold(20): 0.879 RNAshapes: 0.612 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.666 Fold: 0.552 Sensitivity CentroidAlifold(20): 0.504 Fold: 0.491 Positive Predictive Value CentroidAlifold(20): 0.883 Fold: 0.624 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.569 TurboFold(seed): 0.510 Sensitivity CentroidAlifold(20): 0.391 TurboFold(seed): 0.419 Positive Predictive Value CentroidAlifold(20): 0.833 TurboFold(seed): 0.626 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RSpredict(20): 0.541 Sensitivity CentroidAlifold(20): 0.518 RSpredict(20): 0.422 Positive Predictive Value CentroidAlifold(20): 0.877 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.635 Afold: 0.511 Sensitivity CentroidAlifold(20): 0.476 Afold: 0.467 Positive Predictive Value CentroidAlifold(20): 0.850 Afold: 0.564 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAsubopt: 0.544 Sensitivity CentroidAlifold(20): 0.516 RNAsubopt: 0.488 Positive Predictive Value CentroidAlifold(20): 0.879 RNAsubopt: 0.611 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.656 RNASLOpt: 0.463 Sensitivity CentroidAlifold(20): 0.501 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.864 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.720 Cylofold: 0.608 Sensitivity CentroidAlifold(20): 0.566 Cylofold: 0.524 Positive Predictive Value CentroidAlifold(20): 0.919 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 McQFold: 0.508 Sensitivity CentroidAlifold(20): 0.516 McQFold: 0.437 Positive Predictive Value CentroidAlifold(20): 0.879 McQFold: 0.596 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Multilign(20): 0.526 Sensitivity CentroidAlifold(20): 0.518 Multilign(20): 0.437 Positive Predictive Value CentroidAlifold(20): 0.879 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.687 CRWrnafold: 0.546 Sensitivity CentroidAlifold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value CentroidAlifold(20): 0.924 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Pknots: 0.483 Sensitivity CentroidAlifold(20): 0.529 Pknots: 0.439 Positive Predictive Value CentroidAlifold(20): 0.879 Pknots: 0.539 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.502 RNASampler(seed): 0.473 Sensitivity CentroidAlifold(20): 0.332 RNASampler(seed): 0.347 Positive Predictive Value CentroidAlifold(20): 0.763 RNASampler(seed): 0.651 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.14531876181e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.750 Alterna: 0.558 Sensitivity CentroidAlifold(20): 0.608 Alterna: 0.491 Positive Predictive Value CentroidAlifold(20): 0.930 Alterna: 0.643 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Mastr(20): 0.499 Sensitivity CentroidAlifold(20): 0.516 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(20): 0.879 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.681 Vsfold4: 0.445 Sensitivity CentroidAlifold(20): 0.527 Vsfold4: 0.373 Positive Predictive Value CentroidAlifold(20): 0.882 Vsfold4: 0.536 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.604 Murlet(seed): 0.453 Sensitivity CentroidAlifold(20): 0.421 Murlet(seed): 0.238 Positive Predictive Value CentroidAlifold(20): 0.870 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.681 Vsfold5: 0.404 Sensitivity CentroidAlifold(20): 0.527 Vsfold5: 0.345 Positive Predictive Value CentroidAlifold(20): 0.882 Vsfold5: 0.480 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.672 MCFold: 0.396 Sensitivity CentroidAlifold(20): 0.522 MCFold: 0.414 Positive Predictive Value CentroidAlifold(20): 0.869 MCFold: 0.387 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.753 RDfolder: 0.541 Sensitivity CentroidAlifold(20): 0.602 RDfolder: 0.439 Positive Predictive Value CentroidAlifold(20): 0.946 RDfolder: 0.676 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.669 RNAwolf: 0.348 Sensitivity CentroidAlifold(20): 0.511 RNAwolf: 0.328 Positive Predictive Value CentroidAlifold(20): 0.880 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.667 CMfinder(20): 0.521 Sensitivity CentroidAlifold(20): 0.524 CMfinder(20): 0.366 Positive Predictive Value CentroidAlifold(20): 0.853 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.664 NanoFolder: 0.269 Sensitivity CentroidAlifold(20): 0.516 NanoFolder: 0.280 Positive Predictive Value CentroidAlifold(20): 0.859 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.72523032126e-08	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.571 Multilign(seed): 0.542 Sensitivity CentroidAlifold(20): 0.386 Multilign(seed): 0.413 Positive Predictive Value CentroidAlifold(20): 0.851 Multilign(seed): 0.719 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(seed): 0.072 Sensitivity CentroidAlifold(20): 0.514 PPfold(seed): 0.012 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.81788725234e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RSpredict(seed): 0.182 Sensitivity CentroidAlifold(20): 0.518 RSpredict(seed): 0.074 Positive Predictive Value CentroidAlifold(20): 0.877 RSpredict(seed): 0.454 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.632 Carnac(seed): 0.146 Sensitivity CentroidAlifold(20): 0.464 Carnac(seed): 0.021 Positive Predictive Value CentroidAlifold(20): 0.864 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.516 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.879 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidAlifold(20): 0.662 Sensitivity PETfold_2.0(seed): 0.614 CentroidAlifold(20): 0.474 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidAlifold(20): 0.931 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.662 PETfold_2.0(20): 0.647 Sensitivity CentroidAlifold(20): 0.474 PETfold_2.0(20): 0.509 Positive Predictive Value CentroidAlifold(20): 0.931 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(seed)	18 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 CentroidAlifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.597 CentroidAlifold(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.870 CentroidAlifold(20): 0.864 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08		+ PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ContextFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.602 ContextFold: 0.552 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ContextFold: 0.815 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.713 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.600 MXScarna(seed): 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.848 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(seed): 0.597 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.674 PETfold_pre2.0(20): 0.632 Sensitivity PETfold_pre2.0(seed): 0.538 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.846 PETfold_pre2.0(20): 0.806 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 PPfold(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.595 PPfold(20): 0.517 Positive Predictive Value PETfold_pre2.0(seed): 0.864 PPfold(20): 0.819 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 IPknot: 0.587 Sensitivity PETfold_pre2.0(seed): 0.602 IPknot: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.850 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidAlifold(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidAlifold(seed): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.597 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(seed): 0.595 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(seed): 0.864 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(seed): 0.597 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.870 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Sfold: 0.505 Sensitivity PETfold_pre2.0(seed): 0.602 Sfold: 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Sfold: 0.601 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.574 Sensitivity PETfold_pre2.0(seed): 0.606 CentroidHomfold‑LAST: 0.489 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CentroidHomfold‑LAST: 0.680 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Contrafold: 0.565 Sensitivity PETfold_pre2.0(seed): 0.602 Contrafold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Contrafold: 0.650 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAalifold(seed): 0.637 Sensitivity PETfold_pre2.0(seed): 0.570 RNAalifold(seed): 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.811 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 HotKnots: 0.504 Sensitivity PETfold_pre2.0(seed): 0.595 HotKnots: 0.450 Positive Predictive Value PETfold_pre2.0(seed): 0.879 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 MaxExpect: 0.509 Sensitivity PETfold_pre2.0(seed): 0.602 MaxExpect: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.850 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidFold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.602 UNAFold: 0.414 Positive Predictive Value PETfold_pre2.0(seed): 0.850 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(seed): 0.595 PknotsRG: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.879 PknotsRG: 0.636 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ProbKnot: 0.513 Sensitivity PETfold_pre2.0(seed): 0.602 ProbKnot: 0.447 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ProbKnot: 0.590 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(seed): 0.597 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAfold: 0.500 Sensitivity PETfold_pre2.0(seed): 0.602 RNAfold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAfold: 0.573 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(seed): 0.597 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAshapes: 0.491 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAshapes: 0.567 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Fold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.602 Fold: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Fold: 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.645 TurboFold(seed): 0.504 Sensitivity PETfold_pre2.0(seed): 0.511 TurboFold(seed): 0.416 Positive Predictive Value PETfold_pre2.0(seed): 0.818 TurboFold(seed): 0.616 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.669 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.534 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(seed): 0.841 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.639 Afold: 0.453 Sensitivity PETfold_pre2.0(seed): 0.521 Afold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Afold: 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAsubopt: 0.525 Sensitivity PETfold_pre2.0(seed): 0.595 RNAsubopt: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNASLOpt: 0.499 Sensitivity PETfold_pre2.0(seed): 0.595 RNASLOpt: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Cylofold: 0.563 Sensitivity PETfold_pre2.0(seed): 0.609 Cylofold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.871 Cylofold: 0.681 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 McQFold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.602 McQFold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.850 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(seed): 0.616 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	? PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.675 CRWrnafold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.553 CRWrnafold: 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.828 CRWrnafold: 0.599 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Pknots: 0.457 Sensitivity PETfold_pre2.0(seed): 0.595 Pknots: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.594 RNASampler(seed): 0.333 Sensitivity PETfold_pre2.0(seed): 0.453 RNASampler(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.782 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Alterna: 0.545 Sensitivity PETfold_pre2.0(seed): 0.540 Alterna: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(seed): 0.597 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.452 Sensitivity PETfold_pre2.0(seed): 0.605 Vsfold4: 0.371 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.640 Murlet(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.508 Murlet(seed): 0.213 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.403 Sensitivity PETfold_pre2.0(seed): 0.606 Vsfold5: 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 MCFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.579 MCFold: 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.857 MCFold: 0.379 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RDfolder: 0.395 Sensitivity PETfold_pre2.0(seed): 0.588 RDfolder: 0.311 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.514 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAwolf: 0.404 Sensitivity PETfold_pre2.0(seed): 0.602 RNAwolf: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(seed): 0.622 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(seed): 0.885 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 NanoFolder: 0.290 Sensitivity PETfold_pre2.0(seed): 0.605 NanoFolder: 0.301 Positive Predictive Value PETfold_pre2.0(seed): 0.885 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.658 Multilign(seed): 0.533 Sensitivity PETfold_pre2.0(seed): 0.510 Multilign(seed): 0.411 Positive Predictive Value PETfold_pre2.0(seed): 0.851 Multilign(seed): 0.698 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 PPfold(seed): 0.156 Sensitivity PETfold_pre2.0(seed): 0.594 PPfold(seed): 0.036 Positive Predictive Value PETfold_pre2.0(seed): 0.875 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.688 RSpredict(seed): 0.416 Sensitivity PETfold_pre2.0(seed): 0.566 RSpredict(seed): 0.264 Positive Predictive Value PETfold_pre2.0(seed): 0.838 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.687 Carnac(seed): 0.467 Sensitivity PETfold_pre2.0(seed): 0.577 Carnac(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Mastr(seed): 0.034 Sensitivity PETfold_pre2.0(seed): 0.595 Mastr(seed): 0.003 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.775 PETfold_2.0(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.642 PETfold_2.0(seed): 0.642 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
ContextFold	18 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.656 ContextFold: 0.617 Sensitivity CentroidAlifold(20): 0.501 ContextFold: 0.499 Positive Predictive Value CentroidAlifold(20): 0.864 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.32677072069e-08	26 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ContextFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.602 ContextFold: 0.552 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ContextFold: 0.815 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08		+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.696 MXScarna(seed): 0.642 Sensitivity ContextFold: 0.572 MXScarna(seed): 0.536 Positive Predictive Value ContextFold: 0.847 MXScarna(seed): 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.660 RNAalifold(20): 0.645 Sensitivity ContextFold: 0.525 RNAalifold(20): 0.493 Positive Predictive Value ContextFold: 0.835 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26346675981e-08	- PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ContextFold: 0.617 Sensitivity PETfold_pre2.0(20): 0.530 ContextFold: 0.499 Positive Predictive Value PETfold_pre2.0(20): 0.798 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.43573297697e-08	- PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.680 ContextFold: 0.660 Sensitivity PPfold(20): 0.537 ContextFold: 0.525 Positive Predictive Value PPfold(20): 0.865 ContextFold: 0.835 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61876844178e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.563 IPknot: 0.544 Sensitivity ContextFold: 0.466 IPknot: 0.438 Positive Predictive Value ContextFold: 0.681 IPknot: 0.676 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 2.38297003775e-06	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.670 CentroidAlifold(seed): 0.628 Sensitivity ContextFold: 0.552 CentroidAlifold(seed): 0.443 Positive Predictive Value ContextFold: 0.815 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.660 RNASampler(20): 0.575 Sensitivity ContextFold: 0.525 RNASampler(20): 0.431 Positive Predictive Value ContextFold: 0.835 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.660 TurboFold(20): 0.635 Sensitivity ContextFold: 0.525 TurboFold(20): 0.507 Positive Predictive Value ContextFold: 0.835 TurboFold(20): 0.798 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.660 MXScarna(20): 0.564 Sensitivity ContextFold: 0.525 MXScarna(20): 0.456 Positive Predictive Value ContextFold: 0.835 MXScarna(20): 0.703 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.563 Sfold: 0.493 Sensitivity ContextFold: 0.466 Sfold: 0.418 Positive Predictive Value ContextFold: 0.681 Sfold: 0.583 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.662 CentroidHomfold‑LAST: 0.559 Sensitivity ContextFold: 0.547 CentroidHomfold‑LAST: 0.417 Positive Predictive Value ContextFold: 0.806 CentroidHomfold‑LAST: 0.753 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.563 Contrafold: 0.487 Sensitivity ContextFold: 0.466 Contrafold: 0.419 Positive Predictive Value ContextFold: 0.681 Contrafold: 0.568 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.665 RNAalifold(seed): 0.652 Sensitivity ContextFold: 0.549 RNAalifold(seed): 0.506 Positive Predictive Value ContextFold: 0.808 RNAalifold(seed): 0.839 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.28582059552e-06	+ ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.633 HotKnots: 0.549 Sensitivity ContextFold: 0.523 HotKnots: 0.485 Positive Predictive Value ContextFold: 0.769 HotKnots: 0.626 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.563 MaxExpect: 0.473 Sensitivity ContextFold: 0.466 MaxExpect: 0.409 Positive Predictive Value ContextFold: 0.681 MaxExpect: 0.549 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.566 CentroidFold: 0.476 Sensitivity ContextFold: 0.469 CentroidFold: 0.385 Positive Predictive Value ContextFold: 0.684 CentroidFold: 0.591 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.563 UNAFold: 0.469 Sensitivity ContextFold: 0.466 UNAFold: 0.412 Positive Predictive Value ContextFold: 0.681 UNAFold: 0.534 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.509 PknotsRG: 0.474 Sensitivity ContextFold: 0.419 PknotsRG: 0.419 Positive Predictive Value ContextFold: 0.620 PknotsRG: 0.538 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.563 ProbKnot: 0.472 Sensitivity ContextFold: 0.466 ProbKnot: 0.414 Positive Predictive Value ContextFold: 0.681 ProbKnot: 0.539 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.660 Murlet(20): 0.532 Sensitivity ContextFold: 0.525 Murlet(20): 0.394 Positive Predictive Value ContextFold: 0.835 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.563 RNAfold: 0.470 Sensitivity ContextFold: 0.466 RNAfold: 0.413 Positive Predictive Value ContextFold: 0.681 RNAfold: 0.535 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.660 Carnac(20): 0.524 Sensitivity ContextFold: 0.525 Carnac(20): 0.337 Positive Predictive Value ContextFold: 0.835 Carnac(20): 0.820 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.633 RNAshapes: 0.512 Sensitivity ContextFold: 0.523 RNAshapes: 0.447 Positive Predictive Value ContextFold: 0.769 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.563 Fold: 0.436 Sensitivity ContextFold: 0.466 Fold: 0.388 Positive Predictive Value ContextFold: 0.681 Fold: 0.492 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.508 TurboFold(seed): 0.478 Sensitivity ContextFold: 0.396 TurboFold(seed): 0.382 Positive Predictive Value ContextFold: 0.657 TurboFold(seed): 0.603 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.605 RSpredict(20): 0.491 Sensitivity ContextFold: 0.492 RSpredict(20): 0.373 Positive Predictive Value ContextFold: 0.749 RSpredict(20): 0.653 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	= Afold vs ContextFold Matthews Correlation Coefficient Afold: 0.426 ContextFold: 0.424 Sensitivity Afold: 0.385 ContextFold: 0.355 Positive Predictive Value Afold: 0.473 ContextFold: 0.509 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00757664188007	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.633 RNAsubopt: 0.511 Sensitivity ContextFold: 0.523 RNAsubopt: 0.452 Positive Predictive Value ContextFold: 0.769 RNAsubopt: 0.582 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.633 RNASLOpt: 0.489 Sensitivity ContextFold: 0.523 RNASLOpt: 0.393 Positive Predictive Value ContextFold: 0.769 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.675 Cylofold: 0.522 Sensitivity ContextFold: 0.562 Cylofold: 0.436 Positive Predictive Value ContextFold: 0.814 Cylofold: 0.632 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.560 McQFold: 0.392 Sensitivity ContextFold: 0.463 McQFold: 0.333 Positive Predictive Value ContextFold: 0.679 McQFold: 0.462 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.706 Multilign(20): 0.557 Sensitivity ContextFold: 0.565 Multilign(20): 0.472 Positive Predictive Value ContextFold: 0.885 Multilign(20): 0.663 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.690 CRWrnafold: 0.589 Sensitivity ContextFold: 0.579 CRWrnafold: 0.521 Positive Predictive Value ContextFold: 0.827 CRWrnafold: 0.672 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.642 Pknots: 0.491 Sensitivity ContextFold: 0.537 Pknots: 0.445 Positive Predictive Value ContextFold: 0.773 Pknots: 0.549 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.478 RNASampler(seed): 0.317 Sensitivity ContextFold: 0.386 RNASampler(seed): 0.207 Positive Predictive Value ContextFold: 0.596 RNASampler(seed): 0.492 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.690 Alterna: 0.601 Sensitivity ContextFold: 0.587 Alterna: 0.537 Positive Predictive Value ContextFold: 0.819 Alterna: 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.660 Mastr(20): 0.475 Sensitivity ContextFold: 0.525 Mastr(20): 0.308 Positive Predictive Value ContextFold: 0.835 Mastr(20): 0.740 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.93000771886e-09	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.660 Vsfold4: 0.500 Sensitivity ContextFold: 0.549 Vsfold4: 0.418 Positive Predictive Value ContextFold: 0.797 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.522 Murlet(seed): 0.400 Sensitivity ContextFold: 0.413 Murlet(seed): 0.225 Positive Predictive Value ContextFold: 0.665 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.674 Vsfold5: 0.433 Sensitivity ContextFold: 0.563 Vsfold5: 0.373 Positive Predictive Value ContextFold: 0.813 Vsfold5: 0.510 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.603 MCFold: 0.450 Sensitivity ContextFold: 0.506 MCFold: 0.460 Positive Predictive Value ContextFold: 0.724 MCFold: 0.448 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.693 RDfolder: 0.491 Sensitivity ContextFold: 0.581 RDfolder: 0.389 Positive Predictive Value ContextFold: 0.835 RDfolder: 0.632 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.566 RNAwolf: 0.343 Sensitivity ContextFold: 0.469 RNAwolf: 0.318 Positive Predictive Value ContextFold: 0.684 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.788 CMfinder(20): 0.546 Sensitivity ContextFold: 0.640 CMfinder(20): 0.366 Positive Predictive Value ContextFold: 0.972 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.622 NanoFolder: 0.339 Sensitivity ContextFold: 0.512 NanoFolder: 0.350 Positive Predictive Value ContextFold: 0.761 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.517 Multilign(seed): 0.477 Sensitivity ContextFold: 0.421 Multilign(seed): 0.358 Positive Predictive Value ContextFold: 0.640 Multilign(seed): 0.642 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.657 PPfold(seed): 0.100 Sensitivity ContextFold: 0.527 PPfold(seed): 0.019 Positive Predictive Value ContextFold: 0.824 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.667 RSpredict(seed): 0.397 Sensitivity ContextFold: 0.551 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.809 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.672 Carnac(seed): 0.479 Sensitivity ContextFold: 0.553 Carnac(seed): 0.260 Positive Predictive Value ContextFold: 0.816 Carnac(seed): 0.882 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.657 Mastr(seed): 0.000 Sensitivity ContextFold: 0.527 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.824 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.02510705504e-08	? ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.780 PETfold_2.0(seed): 0.769 Sensitivity ContextFold: 0.632 PETfold_2.0(seed): 0.642 Positive Predictive Value ContextFold: 0.968 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.760 PETfold_2.0(20): 0.647 Sensitivity ContextFold: 0.579 PETfold_2.0(20): 0.509 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MXScarna(seed)	38 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.669 MXScarna(seed): 0.642 Sensitivity CentroidAlifold(20): 0.513 MXScarna(seed): 0.528 Positive Predictive Value CentroidAlifold(20): 0.877 MXScarna(seed): 0.784 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.713 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.600 MXScarna(seed): 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.848 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	17 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.696 MXScarna(seed): 0.642 Sensitivity ContextFold: 0.572 MXScarna(seed): 0.536 Positive Predictive Value ContextFold: 0.847 MXScarna(seed): 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08		+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 RNAalifold(20): 0.654 Sensitivity MXScarna(seed): 0.545 RNAalifold(20): 0.502 Positive Predictive Value MXScarna(seed): 0.801 RNAalifold(20): 0.855 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 2.23046259944e-06	- PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.642 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(20): 0.524 MXScarna(seed): 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.791 MXScarna(seed): 0.748 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	- PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.691 MXScarna(seed): 0.629 Sensitivity PPfold(20): 0.544 MXScarna(seed): 0.507 Positive Predictive Value PPfold(20): 0.881 MXScarna(seed): 0.786 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.647 IPknot: 0.620 Sensitivity MXScarna(seed): 0.539 IPknot: 0.513 Positive Predictive Value MXScarna(seed): 0.778 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 7.39132889808e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.657 CentroidAlifold(seed): 0.625 Sensitivity MXScarna(seed): 0.550 CentroidAlifold(seed): 0.446 Positive Predictive Value MXScarna(seed): 0.787 CentroidAlifold(seed): 0.879 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 RNASampler(20): 0.629 Sensitivity MXScarna(seed): 0.545 RNASampler(20): 0.479 Positive Predictive Value MXScarna(seed): 0.801 RNASampler(20): 0.828 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.655 MXScarna(seed): 0.629 Sensitivity TurboFold(20): 0.529 MXScarna(seed): 0.507 Positive Predictive Value TurboFold(20): 0.816 MXScarna(seed): 0.786 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 MXScarna(20): 0.629 Sensitivity MXScarna(seed): 0.545 MXScarna(20): 0.523 Positive Predictive Value MXScarna(seed): 0.801 MXScarna(20): 0.759 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.667 Sfold: 0.570 Sensitivity MXScarna(seed): 0.560 Sfold: 0.490 Positive Predictive Value MXScarna(seed): 0.794 Sfold: 0.665 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.645 CentroidHomfold‑LAST: 0.626 Sensitivity MXScarna(seed): 0.530 CentroidHomfold‑LAST: 0.534 Positive Predictive Value MXScarna(seed): 0.792 CentroidHomfold‑LAST: 0.740 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.00960443857e-07	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.667 Contrafold: 0.599 Sensitivity MXScarna(seed): 0.560 Contrafold: 0.535 Positive Predictive Value MXScarna(seed): 0.794 Contrafold: 0.671 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.643 RNAalifold(seed): 0.631 Sensitivity MXScarna(seed): 0.536 RNAalifold(seed): 0.460 Positive Predictive Value MXScarna(seed): 0.773 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.666 HotKnots: 0.581 Sensitivity MXScarna(seed): 0.554 HotKnots: 0.528 Positive Predictive Value MXScarna(seed): 0.804 HotKnots: 0.643 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.663 MaxExpect: 0.572 Sensitivity MXScarna(seed): 0.557 MaxExpect: 0.506 Positive Predictive Value MXScarna(seed): 0.789 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.657 CentroidFold: 0.578 Sensitivity MXScarna(seed): 0.550 CentroidFold: 0.496 Positive Predictive Value MXScarna(seed): 0.787 CentroidFold: 0.674 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.667 UNAFold: 0.555 Sensitivity MXScarna(seed): 0.560 UNAFold: 0.495 Positive Predictive Value MXScarna(seed): 0.794 UNAFold: 0.625 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.666 PknotsRG: 0.592 Sensitivity MXScarna(seed): 0.554 PknotsRG: 0.537 Positive Predictive Value MXScarna(seed): 0.804 PknotsRG: 0.658 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.654 ProbKnot: 0.550 Sensitivity MXScarna(seed): 0.548 ProbKnot: 0.493 Positive Predictive Value MXScarna(seed): 0.782 ProbKnot: 0.615 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Murlet(20): 0.577 Sensitivity MXScarna(seed): 0.545 Murlet(20): 0.425 Positive Predictive Value MXScarna(seed): 0.801 Murlet(20): 0.788 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.667 RNAfold: 0.561 Sensitivity MXScarna(seed): 0.560 RNAfold: 0.502 Positive Predictive Value MXScarna(seed): 0.794 RNAfold: 0.627 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Carnac(20): 0.580 Sensitivity MXScarna(seed): 0.545 Carnac(20): 0.377 Positive Predictive Value MXScarna(seed): 0.801 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.666 RNAshapes: 0.585 Sensitivity MXScarna(seed): 0.554 RNAshapes: 0.525 Positive Predictive Value MXScarna(seed): 0.804 RNAshapes: 0.657 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.661 Fold: 0.563 Sensitivity MXScarna(seed): 0.556 Fold: 0.507 Positive Predictive Value MXScarna(seed): 0.787 Fold: 0.625 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.548 TurboFold(seed): 0.544 Sensitivity MXScarna(seed): 0.429 TurboFold(seed): 0.439 Positive Predictive Value MXScarna(seed): 0.707 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0173590247318	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.648 RSpredict(20): 0.539 Sensitivity MXScarna(seed): 0.534 RSpredict(20): 0.420 Positive Predictive Value MXScarna(seed): 0.789 RSpredict(20): 0.697 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.669 Afold: 0.574 Sensitivity MXScarna(seed): 0.562 Afold: 0.534 Positive Predictive Value MXScarna(seed): 0.800 Afold: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.666 RNAsubopt: 0.572 Sensitivity MXScarna(seed): 0.554 RNAsubopt: 0.520 Positive Predictive Value MXScarna(seed): 0.804 RNAsubopt: 0.633 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.611 RNASLOpt: 0.533 Sensitivity MXScarna(seed): 0.489 RNASLOpt: 0.431 Positive Predictive Value MXScarna(seed): 0.770 RNASLOpt: 0.666 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.677 Cylofold: 0.617 Sensitivity MXScarna(seed): 0.568 Cylofold: 0.527 Positive Predictive Value MXScarna(seed): 0.811 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.667 McQFold: 0.544 Sensitivity MXScarna(seed): 0.560 McQFold: 0.471 Positive Predictive Value MXScarna(seed): 0.794 McQFold: 0.629 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.658 Multilign(20): 0.561 Sensitivity MXScarna(seed): 0.543 Multilign(20): 0.466 Positive Predictive Value MXScarna(seed): 0.801 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	? MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.610 CRWrnafold: 0.536 Sensitivity MXScarna(seed): 0.490 CRWrnafold: 0.472 Positive Predictive Value MXScarna(seed): 0.765 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.676 Pknots: 0.590 Sensitivity MXScarna(seed): 0.565 Pknots: 0.537 Positive Predictive Value MXScarna(seed): 0.815 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 RNASampler(seed): 0.635 Sensitivity MXScarna(seed): 0.532 RNASampler(seed): 0.484 Positive Predictive Value MXScarna(seed): 0.789 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.725 Alterna: 0.655 Sensitivity MXScarna(seed): 0.609 Alterna: 0.587 Positive Predictive Value MXScarna(seed): 0.869 Alterna: 0.737 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Mastr(20): 0.516 Sensitivity MXScarna(seed): 0.545 Mastr(20): 0.341 Positive Predictive Value MXScarna(seed): 0.801 Mastr(20): 0.786 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.675 Vsfold4: 0.532 Sensitivity MXScarna(seed): 0.566 Vsfold4: 0.456 Positive Predictive Value MXScarna(seed): 0.810 Vsfold4: 0.624 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 Murlet(seed): 0.514 Sensitivity MXScarna(seed): 0.532 Murlet(seed): 0.315 Positive Predictive Value MXScarna(seed): 0.789 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.674 Vsfold5: 0.490 Sensitivity MXScarna(seed): 0.565 Vsfold5: 0.423 Positive Predictive Value MXScarna(seed): 0.808 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.658 MCFold: 0.461 Sensitivity MXScarna(seed): 0.547 MCFold: 0.479 Positive Predictive Value MXScarna(seed): 0.797 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.715 RDfolder: 0.548 Sensitivity MXScarna(seed): 0.599 RDfolder: 0.455 Positive Predictive Value MXScarna(seed): 0.859 RDfolder: 0.671 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAwolf: 0.409 Sensitivity MXScarna(seed): 0.529 RNAwolf: 0.379 Positive Predictive Value MXScarna(seed): 0.770 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.652 CMfinder(20): 0.546 Sensitivity MXScarna(seed): 0.543 CMfinder(20): 0.366 Positive Predictive Value MXScarna(seed): 0.788 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.648 NanoFolder: 0.292 Sensitivity MXScarna(seed): 0.535 NanoFolder: 0.300 Positive Predictive Value MXScarna(seed): 0.790 NanoFolder: 0.294 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.77512146924e-08	? MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.560 Multilign(seed): 0.558 Sensitivity MXScarna(seed): 0.448 Multilign(seed): 0.434 Positive Predictive Value MXScarna(seed): 0.707 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.627 PPfold(seed): 0.092 Sensitivity MXScarna(seed): 0.503 PPfold(seed): 0.016 Positive Predictive Value MXScarna(seed): 0.788 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.661 RSpredict(seed): 0.378 Sensitivity MXScarna(seed): 0.554 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.790 RSpredict(seed): 0.645 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.661 Carnac(seed): 0.404 Sensitivity MXScarna(seed): 0.560 Carnac(seed): 0.181 Positive Predictive Value MXScarna(seed): 0.781 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.666 Mastr(seed): 0.239 Sensitivity MXScarna(seed): 0.554 Mastr(seed): 0.064 Positive Predictive Value MXScarna(seed): 0.804 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MXScarna(seed): 0.682 Sensitivity PETfold_2.0(seed): 0.642 MXScarna(seed): 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 MXScarna(seed): 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MXScarna(seed): 0.563 Sensitivity PETfold_2.0(20): 0.509 MXScarna(seed): 0.456 Positive Predictive Value PETfold_2.0(20): 0.829 MXScarna(seed): 0.703 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAalifold(20)	39 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAalifold(20): 0.646 Sensitivity CentroidAlifold(20): 0.516 RNAalifold(20): 0.499 Positive Predictive Value CentroidAlifold(20): 0.879 RNAalifold(20): 0.838 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(seed): 0.597 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	11 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.660 RNAalifold(20): 0.645 Sensitivity ContextFold: 0.525 RNAalifold(20): 0.493 Positive Predictive Value ContextFold: 0.835 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26346675981e-08	33 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 RNAalifold(20): 0.654 Sensitivity MXScarna(seed): 0.545 RNAalifold(20): 0.502 Positive Predictive Value MXScarna(seed): 0.801 RNAalifold(20): 0.855 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 2.23046259944e-06		- PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.530 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	- PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.691 RNAalifold(20): 0.658 Sensitivity PPfold(20): 0.544 RNAalifold(20): 0.514 Positive Predictive Value PPfold(20): 0.881 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.664 IPknot: 0.601 Sensitivity RNAalifold(20): 0.515 IPknot: 0.485 Positive Predictive Value RNAalifold(20): 0.862 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.646 CentroidAlifold(seed): 0.589 Sensitivity RNAalifold(20): 0.499 CentroidAlifold(seed): 0.379 Positive Predictive Value RNAalifold(20): 0.838 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASampler(20): 0.623 Sensitivity RNAalifold(20): 0.502 RNASampler(20): 0.470 Positive Predictive Value RNAalifold(20): 0.860 RNASampler(20): 0.830 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(20): 0.655 Sensitivity RNAalifold(20): 0.514 TurboFold(20): 0.529 Positive Predictive Value RNAalifold(20): 0.847 TurboFold(20): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0020664790085	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 MXScarna(20): 0.624 Sensitivity RNAalifold(20): 0.502 MXScarna(20): 0.518 Positive Predictive Value RNAalifold(20): 0.860 MXScarna(20): 0.756 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.656 Sfold: 0.587 Sensitivity RNAalifold(20): 0.502 Sfold: 0.490 Positive Predictive Value RNAalifold(20): 0.860 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.685 CentroidHomfold‑LAST: 0.645 Sensitivity RNAalifold(20): 0.541 CentroidHomfold‑LAST: 0.549 Positive Predictive Value RNAalifold(20): 0.872 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.656 Contrafold: 0.551 Sensitivity RNAalifold(20): 0.502 Contrafold: 0.486 Positive Predictive Value RNAalifold(20): 0.860 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.578 RNAalifold(seed): 0.570 Sensitivity RNAalifold(20): 0.414 RNAalifold(seed): 0.351 Positive Predictive Value RNAalifold(20): 0.809 RNAalifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.000112898315885	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.656 HotKnots: 0.556 Sensitivity RNAalifold(20): 0.502 HotKnots: 0.495 Positive Predictive Value RNAalifold(20): 0.860 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.655 MaxExpect: 0.580 Sensitivity RNAalifold(20): 0.504 MaxExpect: 0.503 Positive Predictive Value RNAalifold(20): 0.855 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.646 CentroidFold: 0.537 Sensitivity RNAalifold(20): 0.499 CentroidFold: 0.456 Positive Predictive Value RNAalifold(20): 0.838 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.656 UNAFold: 0.572 Sensitivity RNAalifold(20): 0.502 UNAFold: 0.501 Positive Predictive Value RNAalifold(20): 0.860 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.656 PknotsRG: 0.572 Sensitivity RNAalifold(20): 0.502 PknotsRG: 0.508 Positive Predictive Value RNAalifold(20): 0.860 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.646 ProbKnot: 0.578 Sensitivity RNAalifold(20): 0.488 ProbKnot: 0.516 Positive Predictive Value RNAalifold(20): 0.857 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Murlet(20): 0.577 Sensitivity RNAalifold(20): 0.502 Murlet(20): 0.423 Positive Predictive Value RNAalifold(20): 0.860 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAfold: 0.562 Sensitivity RNAalifold(20): 0.502 RNAfold: 0.497 Positive Predictive Value RNAalifold(20): 0.860 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Carnac(20): 0.577 Sensitivity RNAalifold(20): 0.502 Carnac(20): 0.372 Positive Predictive Value RNAalifold(20): 0.860 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAshapes: 0.567 Sensitivity RNAalifold(20): 0.502 RNAshapes: 0.498 Positive Predictive Value RNAalifold(20): 0.860 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.646 Fold: 0.589 Sensitivity RNAalifold(20): 0.488 Fold: 0.525 Positive Predictive Value RNAalifold(20): 0.857 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 RNAalifold(20): 0.561 Sensitivity TurboFold(seed): 0.454 RNAalifold(20): 0.425 Positive Predictive Value TurboFold(seed): 0.708 RNAalifold(20): 0.744 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.645 RSpredict(20): 0.544 Sensitivity RNAalifold(20): 0.499 RSpredict(20): 0.425 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.611 Afold: 0.530 Sensitivity RNAalifold(20): 0.466 Afold: 0.478 Positive Predictive Value RNAalifold(20): 0.804 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAsubopt: 0.549 Sensitivity RNAalifold(20): 0.502 RNAsubopt: 0.490 Positive Predictive Value RNAalifold(20): 0.860 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.645 RNASLOpt: 0.540 Sensitivity RNAalifold(20): 0.493 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(20): 0.847 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.701 Cylofold: 0.616 Sensitivity RNAalifold(20): 0.543 Cylofold: 0.528 Positive Predictive Value RNAalifold(20): 0.909 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.656 McQFold: 0.539 Sensitivity RNAalifold(20): 0.502 McQFold: 0.462 Positive Predictive Value RNAalifold(20): 0.860 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.666 Multilign(20): 0.561 Sensitivity RNAalifold(20): 0.511 Multilign(20): 0.466 Positive Predictive Value RNAalifold(20): 0.875 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.620 CRWrnafold: 0.546 Sensitivity RNAalifold(20): 0.479 CRWrnafold: 0.483 Positive Predictive Value RNAalifold(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.668 Pknots: 0.514 Sensitivity RNAalifold(20): 0.519 Pknots: 0.467 Positive Predictive Value RNAalifold(20): 0.863 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 RNAalifold(20): 0.493 Sensitivity RNASampler(seed): 0.399 RNAalifold(20): 0.385 Positive Predictive Value RNASampler(seed): 0.739 RNAalifold(20): 0.636 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.729 Alterna: 0.571 Sensitivity RNAalifold(20): 0.590 Alterna: 0.504 Positive Predictive Value RNAalifold(20): 0.907 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(20): 0.514 Sensitivity RNAalifold(20): 0.502 Mastr(20): 0.339 Positive Predictive Value RNAalifold(20): 0.860 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.666 Vsfold4: 0.477 Sensitivity RNAalifold(20): 0.512 Vsfold4: 0.401 Positive Predictive Value RNAalifold(20): 0.870 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.586 Murlet(seed): 0.463 Sensitivity RNAalifold(20): 0.428 Murlet(seed): 0.250 Positive Predictive Value RNAalifold(20): 0.807 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.69956606048e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.666 Vsfold5: 0.417 Sensitivity RNAalifold(20): 0.512 Vsfold5: 0.355 Positive Predictive Value RNAalifold(20): 0.870 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.646 MCFold: 0.401 Sensitivity RNAalifold(20): 0.507 MCFold: 0.418 Positive Predictive Value RNAalifold(20): 0.826 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.720 RDfolder: 0.541 Sensitivity RNAalifold(20): 0.564 RDfolder: 0.440 Positive Predictive Value RNAalifold(20): 0.924 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAwolf: 0.348 Sensitivity RNAalifold(20): 0.503 RNAwolf: 0.328 Positive Predictive Value RNAalifold(20): 0.829 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.756 CMfinder(20): 0.546 Sensitivity RNAalifold(20): 0.591 CMfinder(20): 0.366 Positive Predictive Value RNAalifold(20): 0.970 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.669 NanoFolder: 0.276 Sensitivity RNAalifold(20): 0.527 NanoFolder: 0.286 Positive Predictive Value RNAalifold(20): 0.852 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.608 RNAalifold(20): 0.601 Sensitivity Multilign(seed): 0.468 RNAalifold(20): 0.463 Positive Predictive Value Multilign(seed): 0.795 RNAalifold(20): 0.786 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.664 PPfold(seed): 0.061 Sensitivity RNAalifold(20): 0.515 PPfold(seed): 0.010 Positive Predictive Value RNAalifold(20): 0.862 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.645 RSpredict(seed): 0.191 Sensitivity RNAalifold(20): 0.499 RSpredict(seed): 0.079 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.617 Carnac(seed): 0.186 Sensitivity RNAalifold(20): 0.466 Carnac(seed): 0.035 Positive Predictive Value RNAalifold(20): 0.820 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.502 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.860 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNAalifold(20): 0.654 Sensitivity PETfold_2.0(seed): 0.614 RNAalifold(20): 0.491 Positive Predictive Value PETfold_2.0(seed): 0.946 RNAalifold(20): 0.875 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(20): 0.654 PETfold_2.0(20): 0.647 Sensitivity RNAalifold(20): 0.491 PETfold_2.0(20): 0.509 Positive Predictive Value RNAalifold(20): 0.875 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(20)	18 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.656 PETfold_pre2.0(20): 0.649 Sensitivity CentroidAlifold(20): 0.501 PETfold_pre2.0(20): 0.530 Positive Predictive Value CentroidAlifold(20): 0.864 PETfold_pre2.0(20): 0.798 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64089763604e-07	19 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.674 PETfold_pre2.0(20): 0.632 Sensitivity PETfold_pre2.0(seed): 0.538 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.846 PETfold_pre2.0(20): 0.806 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	18 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ContextFold: 0.617 Sensitivity PETfold_pre2.0(20): 0.530 ContextFold: 0.499 Positive Predictive Value PETfold_pre2.0(20): 0.798 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.43573297697e-08	17 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.642 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(20): 0.524 MXScarna(seed): 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.791 MXScarna(seed): 0.748 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	18 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.530 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08		= PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.649 PETfold_pre2.0(20): 0.649 Sensitivity PPfold(20): 0.517 PETfold_pre2.0(20): 0.532 Positive Predictive Value PPfold(20): 0.819 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00427547442917	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 IPknot: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 IPknot: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 IPknot: 0.614 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidAlifold(seed): 0.533 Sensitivity PETfold_pre2.0(20): 0.530 CentroidAlifold(seed): 0.306 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.530 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(20): 0.532 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(20): 0.530 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(20): 0.798 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Sfold: 0.500 Sensitivity PETfold_pre2.0(20): 0.530 Sfold: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 CentroidHomfold‑LAST: 0.565 Sensitivity PETfold_pre2.0(20): 0.559 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(20): 0.826 CentroidHomfold‑LAST: 0.668 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Contrafold: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.798 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.527 PETfold_pre2.0(20): 0.449 Sensitivity RNAalifold(seed): 0.278 PETfold_pre2.0(20): 0.342 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 HotKnots: 0.474 Sensitivity PETfold_pre2.0(20): 0.530 HotKnots: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.798 HotKnots: 0.535 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MaxExpect: 0.481 Sensitivity PETfold_pre2.0(20): 0.530 MaxExpect: 0.412 Positive Predictive Value PETfold_pre2.0(20): 0.798 MaxExpect: 0.568 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidFold: 0.445 Sensitivity PETfold_pre2.0(20): 0.530 CentroidFold: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 UNAFold: 0.462 Sensitivity PETfold_pre2.0(20): 0.530 UNAFold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 UNAFold: 0.531 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PknotsRG: 0.522 Sensitivity PETfold_pre2.0(20): 0.530 PknotsRG: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.798 PknotsRG: 0.593 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ProbKnot: 0.484 Sensitivity PETfold_pre2.0(20): 0.530 ProbKnot: 0.424 Positive Predictive Value PETfold_pre2.0(20): 0.798 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(20): 0.530 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.798 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAfold: 0.483 Sensitivity PETfold_pre2.0(20): 0.530 RNAfold: 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(20): 0.530 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(20): 0.798 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAshapes: 0.454 Sensitivity PETfold_pre2.0(20): 0.530 RNAshapes: 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Fold: 0.458 Sensitivity PETfold_pre2.0(20): 0.530 Fold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 Fold: 0.521 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.488 TurboFold(seed): 0.437 Sensitivity PETfold_pre2.0(20): 0.375 TurboFold(seed): 0.358 Positive Predictive Value PETfold_pre2.0(20): 0.639 TurboFold(seed): 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.526 Afold: 0.416 Sensitivity PETfold_pre2.0(20): 0.410 Afold: 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.679 Afold: 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAsubopt: 0.505 Sensitivity PETfold_pre2.0(20): 0.530 RNAsubopt: 0.451 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASLOpt: 0.463 Sensitivity PETfold_pre2.0(20): 0.530 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Cylofold: 0.611 Sensitivity PETfold_pre2.0(20): 0.624 Cylofold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.896 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 McQFold: 0.449 Sensitivity PETfold_pre2.0(20): 0.530 McQFold: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(20): 0.564 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.825 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.10198558684e-08	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CRWrnafold: 0.531 Sensitivity PETfold_pre2.0(20): 0.497 CRWrnafold: 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 CRWrnafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Pknots: 0.381 Sensitivity PETfold_pre2.0(20): 0.530 Pknots: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.798 Pknots: 0.431 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.299 PETfold_pre2.0(20): 0.262 Sensitivity RNASampler(seed): 0.214 PETfold_pre2.0(20): 0.195 Positive Predictive Value RNASampler(seed): 0.423 PETfold_pre2.0(20): 0.357 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold4: 0.421 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold4: 0.346 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.449 Murlet(seed): 0.407 Sensitivity PETfold_pre2.0(20): 0.342 Murlet(seed): 0.195 Positive Predictive Value PETfold_pre2.0(20): 0.595 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold5: 0.378 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold5: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold5: 0.450 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.628 MCFold: 0.382 Sensitivity PETfold_pre2.0(20): 0.512 MCFold: 0.393 Positive Predictive Value PETfold_pre2.0(20): 0.775 MCFold: 0.378 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 RDfolder: 0.535 Sensitivity PETfold_pre2.0(20): 0.587 RDfolder: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.920 RDfolder: 0.704 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAwolf: 0.312 Sensitivity PETfold_pre2.0(20): 0.530 RNAwolf: 0.295 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAwolf: 0.338 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(20): 0.564 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(20): 0.826 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.35568223474e-09	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.667 NanoFolder: 0.269 Sensitivity PETfold_pre2.0(20): 0.552 NanoFolder: 0.280 Positive Predictive Value PETfold_pre2.0(20): 0.810 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.443 Multilign(seed): 0.401 Sensitivity PETfold_pre2.0(20): 0.323 Multilign(seed): 0.283 Positive Predictive Value PETfold_pre2.0(20): 0.612 Multilign(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PPfold(seed): 0.077 Sensitivity PETfold_pre2.0(20): 0.532 PPfold(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(seed): 0.294 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(seed): 0.144 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.516 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.400 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.670 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_pre2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_pre2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.647 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(20): 0.509 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.829 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PPfold(20)	21 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.668 PPfold(20): 0.662 Sensitivity CentroidAlifold(20): 0.515 PPfold(20): 0.526 Positive Predictive Value CentroidAlifold(20): 0.870 PPfold(20): 0.837 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 PPfold(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.595 PPfold(20): 0.517 Positive Predictive Value PETfold_pre2.0(seed): 0.864 PPfold(20): 0.819 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	11 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.680 ContextFold: 0.660 Sensitivity PPfold(20): 0.537 ContextFold: 0.525 Positive Predictive Value PPfold(20): 0.865 ContextFold: 0.835 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61876844178e-08	15 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.691 MXScarna(seed): 0.629 Sensitivity PPfold(20): 0.544 MXScarna(seed): 0.507 Positive Predictive Value PPfold(20): 0.881 MXScarna(seed): 0.786 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	15 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.691 RNAalifold(20): 0.658 Sensitivity PPfold(20): 0.544 RNAalifold(20): 0.514 Positive Predictive Value PPfold(20): 0.881 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	17 PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.649 PETfold_pre2.0(20): 0.649 Sensitivity PPfold(20): 0.517 PETfold_pre2.0(20): 0.532 Positive Predictive Value PPfold(20): 0.819 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00427547442917		+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.693 IPknot: 0.601 Sensitivity PPfold(20): 0.548 IPknot: 0.485 Positive Predictive Value PPfold(20): 0.880 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.662 CentroidAlifold(seed): 0.555 Sensitivity PPfold(20): 0.526 CentroidAlifold(seed): 0.335 Positive Predictive Value PPfold(20): 0.837 CentroidAlifold(seed): 0.926 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.691 RNASampler(20): 0.623 Sensitivity PPfold(20): 0.544 RNASampler(20): 0.476 Positive Predictive Value PPfold(20): 0.881 RNASampler(20): 0.821 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.691 TurboFold(20): 0.655 Sensitivity PPfold(20): 0.544 TurboFold(20): 0.529 Positive Predictive Value PPfold(20): 0.881 TurboFold(20): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.691 MXScarna(20): 0.602 Sensitivity PPfold(20): 0.544 MXScarna(20): 0.491 Positive Predictive Value PPfold(20): 0.881 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.691 Sfold: 0.594 Sensitivity PPfold(20): 0.544 Sfold: 0.488 Positive Predictive Value PPfold(20): 0.881 Sfold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.723 CentroidHomfold‑LAST: 0.645 Sensitivity PPfold(20): 0.581 CentroidHomfold‑LAST: 0.549 Positive Predictive Value PPfold(20): 0.905 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.691 Contrafold: 0.588 Sensitivity PPfold(20): 0.544 Contrafold: 0.507 Positive Predictive Value PPfold(20): 0.881 Contrafold: 0.687 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	? RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.581 PPfold(20): 0.576 Sensitivity RNAalifold(seed): 0.362 PPfold(20): 0.423 Positive Predictive Value RNAalifold(seed): 0.938 PPfold(20): 0.790 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.691 HotKnots: 0.555 Sensitivity PPfold(20): 0.544 HotKnots: 0.490 Positive Predictive Value PPfold(20): 0.881 HotKnots: 0.636 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.691 MaxExpect: 0.563 Sensitivity PPfold(20): 0.544 MaxExpect: 0.474 Positive Predictive Value PPfold(20): 0.881 MaxExpect: 0.673 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.662 CentroidFold: 0.487 Sensitivity PPfold(20): 0.526 CentroidFold: 0.413 Positive Predictive Value PPfold(20): 0.837 CentroidFold: 0.581 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.691 UNAFold: 0.555 Sensitivity PPfold(20): 0.544 UNAFold: 0.482 Positive Predictive Value PPfold(20): 0.881 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.691 PknotsRG: 0.588 Sensitivity PPfold(20): 0.544 PknotsRG: 0.516 Positive Predictive Value PPfold(20): 0.881 PknotsRG: 0.676 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.691 ProbKnot: 0.565 Sensitivity PPfold(20): 0.544 ProbKnot: 0.495 Positive Predictive Value PPfold(20): 0.881 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.691 Murlet(20): 0.567 Sensitivity PPfold(20): 0.544 Murlet(20): 0.431 Positive Predictive Value PPfold(20): 0.881 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.691 RNAfold: 0.565 Sensitivity PPfold(20): 0.544 RNAfold: 0.491 Positive Predictive Value PPfold(20): 0.881 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.691 Carnac(20): 0.547 Sensitivity PPfold(20): 0.544 Carnac(20): 0.357 Positive Predictive Value PPfold(20): 0.881 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.691 RNAshapes: 0.557 Sensitivity PPfold(20): 0.544 RNAshapes: 0.486 Positive Predictive Value PPfold(20): 0.881 RNAshapes: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.691 Fold: 0.535 Sensitivity PPfold(20): 0.544 Fold: 0.473 Positive Predictive Value PPfold(20): 0.881 Fold: 0.611 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.596 TurboFold(seed): 0.565 Sensitivity PPfold(20): 0.444 TurboFold(seed): 0.454 Positive Predictive Value PPfold(20): 0.805 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.662 RSpredict(20): 0.521 Sensitivity PPfold(20): 0.526 RSpredict(20): 0.401 Positive Predictive Value PPfold(20): 0.837 RSpredict(20): 0.683 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.623 Afold: 0.611 Sensitivity PPfold(20): 0.484 Afold: 0.548 Positive Predictive Value PPfold(20): 0.806 Afold: 0.685 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.691 RNAsubopt: 0.565 Sensitivity PPfold(20): 0.544 RNAsubopt: 0.495 Positive Predictive Value PPfold(20): 0.881 RNAsubopt: 0.652 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.680 RNASLOpt: 0.540 Sensitivity PPfold(20): 0.537 RNASLOpt: 0.443 Positive Predictive Value PPfold(20): 0.865 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.53487163866e-09	+ PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.756 Cylofold: 0.664 Sensitivity PPfold(20): 0.610 Cylofold: 0.559 Positive Predictive Value PPfold(20): 0.941 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.691 McQFold: 0.583 Sensitivity PPfold(20): 0.544 McQFold: 0.491 Positive Predictive Value PPfold(20): 0.881 McQFold: 0.697 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.723 Multilign(20): 0.596 Sensitivity PPfold(20): 0.581 Multilign(20): 0.507 Positive Predictive Value PPfold(20): 0.905 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.657 CRWrnafold: 0.546 Sensitivity PPfold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value PPfold(20): 0.846 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.691 Pknots: 0.497 Sensitivity PPfold(20): 0.544 Pknots: 0.442 Positive Predictive Value PPfold(20): 0.881 Pknots: 0.565 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.513 PPfold(20): 0.507 Sensitivity RNASampler(seed): 0.359 PPfold(20): 0.365 Positive Predictive Value RNASampler(seed): 0.739 PPfold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.726 Alterna: 0.654 Sensitivity PPfold(20): 0.569 Alterna: 0.569 Positive Predictive Value PPfold(20): 0.933 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.691 Mastr(20): 0.537 Sensitivity PPfold(20): 0.544 Mastr(20): 0.369 Positive Predictive Value PPfold(20): 0.881 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.723 Vsfold4: 0.535 Sensitivity PPfold(20): 0.581 Vsfold4: 0.442 Positive Predictive Value PPfold(20): 0.905 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.576 Murlet(seed): 0.457 Sensitivity PPfold(20): 0.423 Murlet(seed): 0.253 Positive Predictive Value PPfold(20): 0.790 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.723 Vsfold5: 0.470 Sensitivity PPfold(20): 0.581 Vsfold5: 0.400 Positive Predictive Value PPfold(20): 0.905 Vsfold5: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.646 MCFold: 0.412 Sensitivity PPfold(20): 0.509 MCFold: 0.422 Positive Predictive Value PPfold(20): 0.824 MCFold: 0.411 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.7402423548e-08	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.720 RDfolder: 0.511 Sensitivity PPfold(20): 0.562 RDfolder: 0.386 Positive Predictive Value PPfold(20): 0.929 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.663 RNAwolf: 0.343 Sensitivity PPfold(20): 0.528 RNAwolf: 0.325 Positive Predictive Value PPfold(20): 0.836 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.788 CMfinder(20): 0.546 Sensitivity PPfold(20): 0.652 CMfinder(20): 0.366 Positive Predictive Value PPfold(20): 0.955 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.719 NanoFolder: 0.276 Sensitivity PPfold(20): 0.590 NanoFolder: 0.286 Positive Predictive Value PPfold(20): 0.880 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.613 Multilign(seed): 0.608 Sensitivity PPfold(20): 0.453 Multilign(seed): 0.468 Positive Predictive Value PPfold(20): 0.835 Multilign(seed): 0.795 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.693 PPfold(seed): 0.061 Sensitivity PPfold(20): 0.548 PPfold(seed): 0.010 Positive Predictive Value PPfold(20): 0.880 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.662 RSpredict(seed): 0.153 Sensitivity PPfold(20): 0.526 RSpredict(seed): 0.060 Positive Predictive Value PPfold(20): 0.837 RSpredict(seed): 0.402 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.609 Carnac(seed): 0.233 Sensitivity PPfold(20): 0.455 Carnac(seed): 0.055 Positive Predictive Value PPfold(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.691 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.544 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.881 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	? PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
IPknot	21 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.669 IPknot: 0.526 Sensitivity CentroidAlifold(20): 0.511 IPknot: 0.433 Positive Predictive Value CentroidAlifold(20): 0.880 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 IPknot: 0.587 Sensitivity PETfold_pre2.0(seed): 0.602 IPknot: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.850 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	49 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.563 IPknot: 0.544 Sensitivity ContextFold: 0.466 IPknot: 0.438 Positive Predictive Value ContextFold: 0.681 IPknot: 0.676 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 2.38297003775e-06	20 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.647 IPknot: 0.620 Sensitivity MXScarna(seed): 0.539 IPknot: 0.513 Positive Predictive Value MXScarna(seed): 0.778 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 7.39132889808e-08	14 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.664 IPknot: 0.601 Sensitivity RNAalifold(20): 0.515 IPknot: 0.485 Positive Predictive Value RNAalifold(20): 0.862 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	18 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 IPknot: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 IPknot: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 IPknot: 0.614 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	14 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.693 IPknot: 0.601 Sensitivity PPfold(20): 0.548 IPknot: 0.485 Positive Predictive Value PPfold(20): 0.880 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08		- CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 IPknot: 0.593 Sensitivity CentroidAlifold(seed): 0.445 IPknot: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.712 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.59469103578e-08	- RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.609 IPknot: 0.601 Sensitivity RNASampler(20): 0.460 IPknot: 0.485 Positive Predictive Value RNASampler(20): 0.813 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.63100176799e-05	- TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.643 IPknot: 0.601 Sensitivity TurboFold(20): 0.515 IPknot: 0.485 Positive Predictive Value TurboFold(20): 0.809 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	= IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.601 MXScarna(20): 0.596 Sensitivity IPknot: 0.485 MXScarna(20): 0.483 Positive Predictive Value IPknot: 0.751 MXScarna(20): 0.741 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.115206966267	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.554 Sfold: 0.504 Sensitivity IPknot: 0.448 Sfold: 0.427 Positive Predictive Value IPknot: 0.688 Sfold: 0.596 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.635 CentroidHomfold‑LAST: 0.583 Sensitivity IPknot: 0.531 CentroidHomfold‑LAST: 0.437 Positive Predictive Value IPknot: 0.761 CentroidHomfold‑LAST: 0.781 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.554 Contrafold: 0.500 Sensitivity IPknot: 0.448 Contrafold: 0.430 Positive Predictive Value IPknot: 0.688 Contrafold: 0.582 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.648 IPknot: 0.596 Sensitivity RNAalifold(seed): 0.501 IPknot: 0.491 Positive Predictive Value RNAalifold(seed): 0.839 IPknot: 0.725 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.11186924993e-07	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.615 HotKnots: 0.560 Sensitivity IPknot: 0.512 HotKnots: 0.493 Positive Predictive Value IPknot: 0.742 HotKnots: 0.639 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.554 MaxExpect: 0.483 Sensitivity IPknot: 0.448 MaxExpect: 0.418 Positive Predictive Value IPknot: 0.688 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.549 CentroidFold: 0.489 Sensitivity IPknot: 0.446 CentroidFold: 0.396 Positive Predictive Value IPknot: 0.678 CentroidFold: 0.606 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.554 UNAFold: 0.480 Sensitivity IPknot: 0.448 UNAFold: 0.421 Positive Predictive Value IPknot: 0.688 UNAFold: 0.547 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.537 PknotsRG: 0.487 Sensitivity IPknot: 0.426 PknotsRG: 0.430 Positive Predictive Value IPknot: 0.678 PknotsRG: 0.553 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.554 ProbKnot: 0.480 Sensitivity IPknot: 0.448 ProbKnot: 0.422 Positive Predictive Value IPknot: 0.688 ProbKnot: 0.548 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.601 Murlet(20): 0.569 Sensitivity IPknot: 0.485 Murlet(20): 0.428 Positive Predictive Value IPknot: 0.751 Murlet(20): 0.762 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.554 RNAfold: 0.480 Sensitivity IPknot: 0.448 RNAfold: 0.422 Positive Predictive Value IPknot: 0.688 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.601 Carnac(20): 0.558 Sensitivity IPknot: 0.485 Carnac(20): 0.371 Positive Predictive Value IPknot: 0.751 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.615 RNAshapes: 0.526 Sensitivity IPknot: 0.512 RNAshapes: 0.459 Positive Predictive Value IPknot: 0.742 RNAshapes: 0.609 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.554 Fold: 0.448 Sensitivity IPknot: 0.448 Fold: 0.398 Positive Predictive Value IPknot: 0.688 Fold: 0.505 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.542 TurboFold(seed): 0.518 Sensitivity IPknot: 0.416 TurboFold(seed): 0.413 Positive Predictive Value IPknot: 0.712 TurboFold(seed): 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.59581922198e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.535 RSpredict(20): 0.520 Sensitivity IPknot: 0.443 RSpredict(20): 0.398 Positive Predictive Value IPknot: 0.651 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.18891756672e-06	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.494 Afold: 0.443 Sensitivity IPknot: 0.388 Afold: 0.400 Positive Predictive Value IPknot: 0.630 Afold: 0.492 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.615 RNAsubopt: 0.528 Sensitivity IPknot: 0.512 RNAsubopt: 0.466 Positive Predictive Value IPknot: 0.742 RNAsubopt: 0.603 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.604 RNASLOpt: 0.489 Sensitivity IPknot: 0.503 RNASLOpt: 0.393 Positive Predictive Value IPknot: 0.728 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.642 Cylofold: 0.533 Sensitivity IPknot: 0.540 Cylofold: 0.447 Positive Predictive Value IPknot: 0.771 Cylofold: 0.644 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.552 McQFold: 0.410 Sensitivity IPknot: 0.445 McQFold: 0.348 Positive Predictive Value IPknot: 0.685 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.620 Multilign(20): 0.577 Sensitivity IPknot: 0.516 Multilign(20): 0.488 Positive Predictive Value IPknot: 0.749 Multilign(20): 0.688 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.654 CRWrnafold: 0.585 Sensitivity IPknot: 0.559 CRWrnafold: 0.522 Positive Predictive Value IPknot: 0.773 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.654 Pknots: 0.515 Sensitivity IPknot: 0.552 Pknots: 0.464 Positive Predictive Value IPknot: 0.780 Pknots: 0.579 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.547 RNASampler(seed): 0.447 Sensitivity IPknot: 0.416 RNASampler(seed): 0.299 Positive Predictive Value IPknot: 0.724 RNASampler(seed): 0.673 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.683 Alterna: 0.589 Sensitivity IPknot: 0.568 Alterna: 0.527 Positive Predictive Value IPknot: 0.829 Alterna: 0.669 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.601 Mastr(20): 0.521 Sensitivity IPknot: 0.485 Mastr(20): 0.352 Positive Predictive Value IPknot: 0.751 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.650 Vsfold4: 0.505 Sensitivity IPknot: 0.554 Vsfold4: 0.424 Positive Predictive Value IPknot: 0.769 Vsfold4: 0.610 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.570 Murlet(seed): 0.421 Sensitivity IPknot: 0.442 Murlet(seed): 0.241 Positive Predictive Value IPknot: 0.741 Murlet(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.644 Vsfold5: 0.446 Sensitivity IPknot: 0.546 Vsfold5: 0.386 Positive Predictive Value IPknot: 0.765 Vsfold5: 0.524 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.610 MCFold: 0.455 Sensitivity IPknot: 0.517 MCFold: 0.466 Positive Predictive Value IPknot: 0.726 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.661 RDfolder: 0.500 Sensitivity IPknot: 0.559 RDfolder: 0.393 Positive Predictive Value IPknot: 0.791 RDfolder: 0.648 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.549 RNAwolf: 0.356 Sensitivity IPknot: 0.446 RNAwolf: 0.331 Positive Predictive Value IPknot: 0.678 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.645 CMfinder(20): 0.546 Sensitivity IPknot: 0.549 CMfinder(20): 0.366 Positive Predictive Value IPknot: 0.763 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.633 NanoFolder: 0.339 Sensitivity IPknot: 0.542 NanoFolder: 0.350 Positive Predictive Value IPknot: 0.743 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.604 Multilign(seed): 0.526 Sensitivity IPknot: 0.455 Multilign(seed): 0.402 Positive Predictive Value IPknot: 0.807 Multilign(seed): 0.695 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.629 PPfold(seed): 0.092 Sensitivity IPknot: 0.506 PPfold(seed): 0.016 Positive Predictive Value IPknot: 0.787 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.599 RSpredict(seed): 0.395 Sensitivity IPknot: 0.501 RSpredict(seed): 0.246 Positive Predictive Value IPknot: 0.717 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.601 Carnac(seed): 0.461 Sensitivity IPknot: 0.495 Carnac(seed): 0.241 Positive Predictive Value IPknot: 0.730 Carnac(seed): 0.882 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.29976619895e-09	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.629 Mastr(seed): 0.000 Sensitivity IPknot: 0.506 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.787 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	? CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 IPknot: 0.610 Sensitivity PETfold_2.0(seed): 0.642 IPknot: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 IPknot: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 IPknot: 0.401 Sensitivity PETfold_2.0(20): 0.509 IPknot: 0.298 Positive Predictive Value PETfold_2.0(20): 0.829 IPknot: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidAlifold(seed)	39 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 CentroidAlifold(seed): 0.589 Sensitivity CentroidAlifold(20): 0.516 CentroidAlifold(seed): 0.379 Positive Predictive Value CentroidAlifold(20): 0.879 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidAlifold(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidAlifold(seed): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.670 CentroidAlifold(seed): 0.628 Sensitivity ContextFold: 0.552 CentroidAlifold(seed): 0.443 Positive Predictive Value ContextFold: 0.815 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	60 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.657 CentroidAlifold(seed): 0.625 Sensitivity MXScarna(seed): 0.550 CentroidAlifold(seed): 0.446 Positive Predictive Value MXScarna(seed): 0.787 CentroidAlifold(seed): 0.879 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.646 CentroidAlifold(seed): 0.589 Sensitivity RNAalifold(20): 0.499 CentroidAlifold(seed): 0.379 Positive Predictive Value RNAalifold(20): 0.838 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidAlifold(seed): 0.533 Sensitivity PETfold_pre2.0(20): 0.530 CentroidAlifold(seed): 0.306 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	21 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.662 CentroidAlifold(seed): 0.555 Sensitivity PPfold(20): 0.526 CentroidAlifold(seed): 0.335 Positive Predictive Value PPfold(20): 0.837 CentroidAlifold(seed): 0.926 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	29 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 IPknot: 0.593 Sensitivity CentroidAlifold(seed): 0.445 IPknot: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.712 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.59469103578e-08		- RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 CentroidAlifold(seed): 0.589 Sensitivity RNASampler(20): 0.466 CentroidAlifold(seed): 0.379 Positive Predictive Value RNASampler(20): 0.800 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.85233844192e-08	- TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.625 CentroidAlifold(seed): 0.555 Sensitivity TurboFold(20): 0.518 CentroidAlifold(seed): 0.335 Positive Predictive Value TurboFold(20): 0.759 CentroidAlifold(seed): 0.926 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	- MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.617 CentroidAlifold(seed): 0.589 Sensitivity MXScarna(20): 0.514 CentroidAlifold(seed): 0.379 Positive Predictive Value MXScarna(20): 0.743 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 Sfold: 0.562 Sensitivity CentroidAlifold(seed): 0.443 Sfold: 0.482 Positive Predictive Value CentroidAlifold(seed): 0.880 Sfold: 0.657 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 CentroidAlifold(seed): 0.563 Sensitivity CentroidHomfold‑LAST: 0.503 CentroidAlifold(seed): 0.345 Positive Predictive Value CentroidHomfold‑LAST: 0.711 CentroidAlifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 Contrafold: 0.586 Sensitivity CentroidAlifold(seed): 0.443 Contrafold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.880 Contrafold: 0.658 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.675 RNAalifold(seed): 0.625 Sensitivity CentroidAlifold(seed): 0.525 RNAalifold(seed): 0.449 Positive Predictive Value CentroidAlifold(seed): 0.870 RNAalifold(seed): 0.871 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 HotKnots: 0.568 Sensitivity CentroidAlifold(seed): 0.397 HotKnots: 0.516 Positive Predictive Value CentroidAlifold(seed): 0.889 HotKnots: 0.630 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.626 MaxExpect: 0.565 Sensitivity CentroidAlifold(seed): 0.446 MaxExpect: 0.498 Positive Predictive Value CentroidAlifold(seed): 0.879 MaxExpect: 0.641 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 CentroidFold: 0.577 Sensitivity CentroidAlifold(seed): 0.443 CentroidFold: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.880 CentroidFold: 0.672 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 UNAFold: 0.546 Sensitivity CentroidAlifold(seed): 0.443 UNAFold: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.880 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 PknotsRG: 0.585 Sensitivity CentroidAlifold(seed): 0.397 PknotsRG: 0.528 Positive Predictive Value CentroidAlifold(seed): 0.889 PknotsRG: 0.652 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 2.38297003775e-06	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 ProbKnot: 0.544 Sensitivity CentroidAlifold(seed): 0.448 ProbKnot: 0.486 Positive Predictive Value CentroidAlifold(seed): 0.890 ProbKnot: 0.611 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Murlet(20): 0.582 Sensitivity CentroidAlifold(seed): 0.379 Murlet(20): 0.430 Positive Predictive Value CentroidAlifold(seed): 0.920 Murlet(20): 0.793 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 1.70900654697e-06	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 RNAfold: 0.553 Sensitivity CentroidAlifold(seed): 0.443 RNAfold: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.880 RNAfold: 0.620 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Carnac(20): 0.579 Sensitivity CentroidAlifold(seed): 0.379 Carnac(20): 0.374 Positive Predictive Value CentroidAlifold(seed): 0.920 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 9.291770879e-07	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RNAshapes: 0.565 Sensitivity CentroidAlifold(seed): 0.397 RNAshapes: 0.505 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAshapes: 0.636 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.628 Fold: 0.554 Sensitivity CentroidAlifold(seed): 0.449 Fold: 0.498 Positive Predictive Value CentroidAlifold(seed): 0.879 Fold: 0.618 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 TurboFold(seed): 0.547 Sensitivity CentroidAlifold(seed): 0.401 TurboFold(seed): 0.452 Positive Predictive Value CentroidAlifold(seed): 0.927 TurboFold(seed): 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RSpredict(20): 0.541 Sensitivity CentroidAlifold(seed): 0.383 RSpredict(20): 0.422 Positive Predictive Value CentroidAlifold(seed): 0.922 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.599 Afold: 0.559 Sensitivity CentroidAlifold(seed): 0.418 Afold: 0.520 Positive Predictive Value CentroidAlifold(seed): 0.861 Afold: 0.605 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RNAsubopt: 0.565 Sensitivity CentroidAlifold(seed): 0.397 RNAsubopt: 0.513 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.558 RNASLOpt: 0.499 Sensitivity CentroidAlifold(seed): 0.334 RNASLOpt: 0.408 Positive Predictive Value CentroidAlifold(seed): 0.936 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	= CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 Cylofold: 0.611 Sensitivity CentroidAlifold(seed): 0.417 Cylofold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.928 Cylofold: 0.719 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0417598136925	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 McQFold: 0.529 Sensitivity CentroidAlifold(seed): 0.443 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.880 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.576 Multilign(20): 0.526 Sensitivity CentroidAlifold(seed): 0.359 Multilign(20): 0.437 Positive Predictive Value CentroidAlifold(seed): 0.927 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.54865340847e-08	? CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.578 CRWrnafold: 0.536 Sensitivity CentroidAlifold(seed): 0.343 CRWrnafold: 0.472 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.597 Pknots: 0.560 Sensitivity CentroidAlifold(seed): 0.398 Pknots: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.902 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.639 RNASampler(seed): 0.586 Sensitivity CentroidAlifold(seed): 0.476 RNASampler(seed): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.862 RNASampler(seed): 0.787 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	- Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.650 CentroidAlifold(seed): 0.592 Sensitivity Alterna: 0.583 CentroidAlifold(seed): 0.415 Positive Predictive Value Alterna: 0.733 CentroidAlifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Mastr(20): 0.499 Sensitivity CentroidAlifold(seed): 0.379 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.920 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold4: 0.499 Sensitivity CentroidAlifold(seed): 0.393 Vsfold4: 0.425 Positive Predictive Value CentroidAlifold(seed): 0.887 Vsfold4: 0.591 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.677 Murlet(seed): 0.503 Sensitivity CentroidAlifold(seed): 0.517 Murlet(seed): 0.299 Positive Predictive Value CentroidAlifold(seed): 0.892 Murlet(seed): 0.851 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.592 Vsfold5: 0.468 Sensitivity CentroidAlifold(seed): 0.396 Vsfold5: 0.405 Positive Predictive Value CentroidAlifold(seed): 0.888 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.596 MCFold: 0.457 Sensitivity CentroidAlifold(seed): 0.396 MCFold: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.901 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 RDfolder: 0.548 Sensitivity CentroidAlifold(seed): 0.427 RDfolder: 0.454 Positive Predictive Value CentroidAlifold(seed): 0.873 RDfolder: 0.671 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 RNAwolf: 0.416 Sensitivity CentroidAlifold(seed): 0.445 RNAwolf: 0.385 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	= CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidAlifold(seed): 0.510 Sensitivity CMfinder(20): 0.366 CentroidAlifold(seed): 0.288 Positive Predictive Value CMfinder(20): 0.748 CentroidAlifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0014244499658	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.536 NanoFolder: 0.290 Sensitivity CentroidAlifold(seed): 0.308 NanoFolder: 0.301 Positive Predictive Value CentroidAlifold(seed): 0.940 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.643 Multilign(seed): 0.578 Sensitivity CentroidAlifold(seed): 0.454 Multilign(seed): 0.454 Positive Predictive Value CentroidAlifold(seed): 0.917 Multilign(seed): 0.743 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.575 PPfold(seed): 0.148 Sensitivity CentroidAlifold(seed): 0.351 PPfold(seed): 0.032 Positive Predictive Value CentroidAlifold(seed): 0.947 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.626 RSpredict(seed): 0.373 Sensitivity CentroidAlifold(seed): 0.447 RSpredict(seed): 0.218 Positive Predictive Value CentroidAlifold(seed): 0.880 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Carnac(seed): 0.396 Sensitivity CentroidAlifold(seed): 0.529 Carnac(seed): 0.173 Positive Predictive Value CentroidAlifold(seed): 0.883 Carnac(seed): 0.905 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 Mastr(seed): 0.219 Sensitivity CentroidAlifold(seed): 0.397 Mastr(seed): 0.055 Positive Predictive Value CentroidAlifold(seed): 0.889 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidAlifold(seed): 0.618 Sensitivity PETfold_2.0(seed): 0.642 CentroidAlifold(seed): 0.432 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidAlifold(seed): 0.484 Sensitivity PETfold_2.0(20): 0.509 CentroidAlifold(seed): 0.281 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidAlifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASampler(20)	39 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNASampler(20): 0.609 Sensitivity CentroidAlifold(20): 0.516 RNASampler(20): 0.466 Positive Predictive Value CentroidAlifold(20): 0.879 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.597 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	11 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.660 RNASampler(20): 0.575 Sensitivity ContextFold: 0.525 RNASampler(20): 0.431 Positive Predictive Value ContextFold: 0.835 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.20167918023e-08	33 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 RNASampler(20): 0.629 Sensitivity MXScarna(seed): 0.545 RNASampler(20): 0.479 Positive Predictive Value MXScarna(seed): 0.801 RNASampler(20): 0.828 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASampler(20): 0.623 Sensitivity RNAalifold(20): 0.502 RNASampler(20): 0.470 Positive Predictive Value RNAalifold(20): 0.860 RNASampler(20): 0.830 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.530 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.20167918023e-08	15 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.691 RNASampler(20): 0.623 Sensitivity PPfold(20): 0.544 RNASampler(20): 0.476 Positive Predictive Value PPfold(20): 0.881 RNASampler(20): 0.821 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	14 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.609 IPknot: 0.601 Sensitivity RNASampler(20): 0.460 IPknot: 0.485 Positive Predictive Value RNASampler(20): 0.813 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.63100176799e-05	39 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 CentroidAlifold(seed): 0.589 Sensitivity RNASampler(20): 0.466 CentroidAlifold(seed): 0.379 Positive Predictive Value RNASampler(20): 0.800 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.85233844192e-08		- TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.655 RNASampler(20): 0.623 Sensitivity TurboFold(20): 0.529 RNASampler(20): 0.476 Positive Predictive Value TurboFold(20): 0.816 RNASampler(20): 0.821 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.75835195567e-08	= MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.624 RNASampler(20): 0.623 Sensitivity MXScarna(20): 0.518 RNASampler(20): 0.470 Positive Predictive Value MXScarna(20): 0.756 RNASampler(20): 0.830 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.925038393872	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.623 Sfold: 0.587 Sensitivity RNASampler(20): 0.470 Sfold: 0.490 Positive Predictive Value RNASampler(20): 0.830 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.659 CentroidHomfold‑LAST: 0.645 Sensitivity RNASampler(20): 0.507 CentroidHomfold‑LAST: 0.549 Positive Predictive Value RNASampler(20): 0.861 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.53530931377e-06	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.623 Contrafold: 0.551 Sensitivity RNASampler(20): 0.470 Contrafold: 0.486 Positive Predictive Value RNASampler(20): 0.830 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 RNASampler(20): 0.563 Sensitivity RNAalifold(seed): 0.351 RNASampler(20): 0.411 Positive Predictive Value RNAalifold(seed): 0.930 RNASampler(20): 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.23133840878e-05	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.623 HotKnots: 0.556 Sensitivity RNASampler(20): 0.470 HotKnots: 0.495 Positive Predictive Value RNASampler(20): 0.830 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.625 MaxExpect: 0.580 Sensitivity RNASampler(20): 0.475 MaxExpect: 0.503 Positive Predictive Value RNASampler(20): 0.826 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.609 CentroidFold: 0.537 Sensitivity RNASampler(20): 0.466 CentroidFold: 0.456 Positive Predictive Value RNASampler(20): 0.800 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.623 UNAFold: 0.572 Sensitivity RNASampler(20): 0.470 UNAFold: 0.501 Positive Predictive Value RNASampler(20): 0.830 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.623 PknotsRG: 0.572 Sensitivity RNASampler(20): 0.470 PknotsRG: 0.508 Positive Predictive Value RNASampler(20): 0.830 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.613 ProbKnot: 0.578 Sensitivity RNASampler(20): 0.455 ProbKnot: 0.516 Positive Predictive Value RNASampler(20): 0.830 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Murlet(20): 0.577 Sensitivity RNASampler(20): 0.470 Murlet(20): 0.423 Positive Predictive Value RNASampler(20): 0.830 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.623 RNAfold: 0.562 Sensitivity RNASampler(20): 0.470 RNAfold: 0.497 Positive Predictive Value RNASampler(20): 0.830 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Carnac(20): 0.577 Sensitivity RNASampler(20): 0.470 Carnac(20): 0.372 Positive Predictive Value RNASampler(20): 0.830 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.623 RNAshapes: 0.567 Sensitivity RNASampler(20): 0.470 RNAshapes: 0.498 Positive Predictive Value RNASampler(20): 0.830 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.613 Fold: 0.589 Sensitivity RNASampler(20): 0.455 Fold: 0.525 Positive Predictive Value RNASampler(20): 0.830 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.584 TurboFold(seed): 0.565 Sensitivity RNASampler(20): 0.438 TurboFold(seed): 0.454 Positive Predictive Value RNASampler(20): 0.784 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.612 RSpredict(20): 0.544 Sensitivity RNASampler(20): 0.471 RSpredict(20): 0.425 Positive Predictive Value RNASampler(20): 0.798 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.602 Afold: 0.530 Sensitivity RNASampler(20): 0.455 Afold: 0.478 Positive Predictive Value RNASampler(20): 0.801 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.623 RNAsubopt: 0.549 Sensitivity RNASampler(20): 0.470 RNAsubopt: 0.490 Positive Predictive Value RNASampler(20): 0.830 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.575 RNASLOpt: 0.540 Sensitivity RNASampler(20): 0.431 RNASLOpt: 0.443 Positive Predictive Value RNASampler(20): 0.771 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.673 Cylofold: 0.616 Sensitivity RNASampler(20): 0.507 Cylofold: 0.528 Positive Predictive Value RNASampler(20): 0.896 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.623 McQFold: 0.539 Sensitivity RNASampler(20): 0.470 McQFold: 0.462 Positive Predictive Value RNASampler(20): 0.830 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.638 Multilign(20): 0.561 Sensitivity RNASampler(20): 0.474 Multilign(20): 0.466 Positive Predictive Value RNASampler(20): 0.863 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.618 CRWrnafold: 0.546 Sensitivity RNASampler(20): 0.462 CRWrnafold: 0.483 Positive Predictive Value RNASampler(20): 0.832 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.639 Pknots: 0.514 Sensitivity RNASampler(20): 0.488 Pknots: 0.467 Positive Predictive Value RNASampler(20): 0.842 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 RNASampler(20): 0.528 Sensitivity RNASampler(seed): 0.399 RNASampler(20): 0.426 Positive Predictive Value RNASampler(seed): 0.739 RNASampler(20): 0.660 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.767 Alterna: 0.571 Sensitivity RNASampler(20): 0.620 Alterna: 0.504 Positive Predictive Value RNASampler(20): 0.953 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Mastr(20): 0.514 Sensitivity RNASampler(20): 0.470 Mastr(20): 0.339 Positive Predictive Value RNASampler(20): 0.830 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.637 Vsfold4: 0.477 Sensitivity RNASampler(20): 0.482 Vsfold4: 0.401 Positive Predictive Value RNASampler(20): 0.846 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.581 Murlet(seed): 0.463 Sensitivity RNASampler(20): 0.429 Murlet(seed): 0.250 Positive Predictive Value RNASampler(20): 0.790 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.637 Vsfold5: 0.417 Sensitivity RNASampler(20): 0.482 Vsfold5: 0.355 Positive Predictive Value RNASampler(20): 0.846 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.617 MCFold: 0.401 Sensitivity RNASampler(20): 0.482 MCFold: 0.418 Positive Predictive Value RNASampler(20): 0.795 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.748 RDfolder: 0.541 Sensitivity RNASampler(20): 0.592 RDfolder: 0.440 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.585 RNAwolf: 0.348 Sensitivity RNASampler(20): 0.448 RNAwolf: 0.328 Positive Predictive Value RNASampler(20): 0.768 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.607 CMfinder(20): 0.546 Sensitivity RNASampler(20): 0.451 CMfinder(20): 0.366 Positive Predictive Value RNASampler(20): 0.822 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.604 NanoFolder: 0.276 Sensitivity RNASampler(20): 0.458 NanoFolder: 0.286 Positive Predictive Value RNASampler(20): 0.801 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.608 RNASampler(20): 0.597 Sensitivity Multilign(seed): 0.468 RNASampler(20): 0.447 Positive Predictive Value Multilign(seed): 0.795 RNASampler(20): 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 PPfold(seed): 0.061 Sensitivity RNASampler(20): 0.460 PPfold(seed): 0.010 Positive Predictive Value RNASampler(20): 0.813 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.612 RSpredict(seed): 0.191 Sensitivity RNASampler(20): 0.471 RSpredict(seed): 0.079 Positive Predictive Value RNASampler(20): 0.798 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.613 Carnac(seed): 0.186 Sensitivity RNASampler(20): 0.460 Carnac(seed): 0.035 Positive Predictive Value RNASampler(20): 0.820 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.623 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.470 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.830 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNASampler(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(seed): 0.946 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASampler(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
TurboFold(20)	21 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.668 TurboFold(20): 0.625 Sensitivity CentroidAlifold(20): 0.515 TurboFold(20): 0.518 Positive Predictive Value CentroidAlifold(20): 0.870 TurboFold(20): 0.759 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	17 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(seed): 0.595 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(seed): 0.864 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	11 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.660 TurboFold(20): 0.635 Sensitivity ContextFold: 0.525 TurboFold(20): 0.507 Positive Predictive Value ContextFold: 0.835 TurboFold(20): 0.798 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	15 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.655 MXScarna(seed): 0.629 Sensitivity TurboFold(20): 0.529 MXScarna(seed): 0.507 Positive Predictive Value TurboFold(20): 0.816 MXScarna(seed): 0.786 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(20): 0.655 Sensitivity RNAalifold(20): 0.514 TurboFold(20): 0.529 Positive Predictive Value RNAalifold(20): 0.847 TurboFold(20): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0020664790085	17 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(20): 0.532 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	15 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.691 TurboFold(20): 0.655 Sensitivity PPfold(20): 0.544 TurboFold(20): 0.529 Positive Predictive Value PPfold(20): 0.881 TurboFold(20): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	14 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.643 IPknot: 0.601 Sensitivity TurboFold(20): 0.515 IPknot: 0.485 Positive Predictive Value TurboFold(20): 0.809 IPknot: 0.751 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	21 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.625 CentroidAlifold(seed): 0.555 Sensitivity TurboFold(20): 0.518 CentroidAlifold(seed): 0.335 Positive Predictive Value TurboFold(20): 0.759 CentroidAlifold(seed): 0.926 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.655 RNASampler(20): 0.623 Sensitivity TurboFold(20): 0.529 RNASampler(20): 0.476 Positive Predictive Value TurboFold(20): 0.816 RNASampler(20): 0.821 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.75835195567e-08		+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.655 MXScarna(20): 0.602 Sensitivity TurboFold(20): 0.529 MXScarna(20): 0.491 Positive Predictive Value TurboFold(20): 0.816 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.655 Sfold: 0.594 Sensitivity TurboFold(20): 0.529 Sfold: 0.488 Positive Predictive Value TurboFold(20): 0.816 Sfold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.681 CentroidHomfold‑LAST: 0.645 Sensitivity TurboFold(20): 0.558 CentroidHomfold‑LAST: 0.549 Positive Predictive Value TurboFold(20): 0.836 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.655 Contrafold: 0.588 Sensitivity TurboFold(20): 0.529 Contrafold: 0.507 Positive Predictive Value TurboFold(20): 0.816 Contrafold: 0.687 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	? TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 RNAalifold(seed): 0.581 Sensitivity TurboFold(20): 0.454 RNAalifold(seed): 0.362 Positive Predictive Value TurboFold(20): 0.751 RNAalifold(seed): 0.938 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.655 HotKnots: 0.555 Sensitivity TurboFold(20): 0.529 HotKnots: 0.490 Positive Predictive Value TurboFold(20): 0.816 HotKnots: 0.636 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.655 MaxExpect: 0.563 Sensitivity TurboFold(20): 0.529 MaxExpect: 0.474 Positive Predictive Value TurboFold(20): 0.816 MaxExpect: 0.673 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.625 CentroidFold: 0.487 Sensitivity TurboFold(20): 0.518 CentroidFold: 0.413 Positive Predictive Value TurboFold(20): 0.759 CentroidFold: 0.581 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.655 UNAFold: 0.555 Sensitivity TurboFold(20): 0.529 UNAFold: 0.482 Positive Predictive Value TurboFold(20): 0.816 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.655 PknotsRG: 0.588 Sensitivity TurboFold(20): 0.529 PknotsRG: 0.516 Positive Predictive Value TurboFold(20): 0.816 PknotsRG: 0.676 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.655 ProbKnot: 0.565 Sensitivity TurboFold(20): 0.529 ProbKnot: 0.495 Positive Predictive Value TurboFold(20): 0.816 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Murlet(20): 0.567 Sensitivity TurboFold(20): 0.529 Murlet(20): 0.431 Positive Predictive Value TurboFold(20): 0.816 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.655 RNAfold: 0.565 Sensitivity TurboFold(20): 0.529 RNAfold: 0.491 Positive Predictive Value TurboFold(20): 0.816 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Carnac(20): 0.547 Sensitivity TurboFold(20): 0.529 Carnac(20): 0.357 Positive Predictive Value TurboFold(20): 0.816 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.655 RNAshapes: 0.557 Sensitivity TurboFold(20): 0.529 RNAshapes: 0.486 Positive Predictive Value TurboFold(20): 0.816 RNAshapes: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.655 Fold: 0.535 Sensitivity TurboFold(20): 0.529 Fold: 0.473 Positive Predictive Value TurboFold(20): 0.816 Fold: 0.611 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.70887622364e-08	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.578 TurboFold(seed): 0.565 Sensitivity TurboFold(20): 0.454 TurboFold(seed): 0.454 Positive Predictive Value TurboFold(20): 0.741 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.625 RSpredict(20): 0.521 Sensitivity TurboFold(20): 0.518 RSpredict(20): 0.401 Positive Predictive Value TurboFold(20): 0.759 RSpredict(20): 0.683 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.646 Afold: 0.611 Sensitivity TurboFold(20): 0.535 Afold: 0.548 Positive Predictive Value TurboFold(20): 0.783 Afold: 0.685 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.655 RNAsubopt: 0.565 Sensitivity TurboFold(20): 0.529 RNAsubopt: 0.495 Positive Predictive Value TurboFold(20): 0.816 RNAsubopt: 0.652 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.635 RNASLOpt: 0.540 Sensitivity TurboFold(20): 0.507 RNASLOpt: 0.443 Positive Predictive Value TurboFold(20): 0.798 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.725 Cylofold: 0.664 Sensitivity TurboFold(20): 0.590 Cylofold: 0.559 Positive Predictive Value TurboFold(20): 0.895 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.655 McQFold: 0.583 Sensitivity TurboFold(20): 0.529 McQFold: 0.491 Positive Predictive Value TurboFold(20): 0.816 McQFold: 0.697 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.681 Multilign(20): 0.596 Sensitivity TurboFold(20): 0.558 Multilign(20): 0.507 Positive Predictive Value TurboFold(20): 0.836 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.570 CRWrnafold: 0.546 Sensitivity TurboFold(20): 0.453 CRWrnafold: 0.483 Positive Predictive Value TurboFold(20): 0.723 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.655 Pknots: 0.497 Sensitivity TurboFold(20): 0.529 Pknots: 0.442 Positive Predictive Value TurboFold(20): 0.816 Pknots: 0.565 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	? TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.532 RNASampler(seed): 0.513 Sensitivity TurboFold(20): 0.425 RNASampler(seed): 0.359 Positive Predictive Value TurboFold(20): 0.670 RNASampler(seed): 0.739 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.721 Alterna: 0.654 Sensitivity TurboFold(20): 0.602 Alterna: 0.569 Positive Predictive Value TurboFold(20): 0.871 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Mastr(20): 0.537 Sensitivity TurboFold(20): 0.529 Mastr(20): 0.369 Positive Predictive Value TurboFold(20): 0.816 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.681 Vsfold4: 0.535 Sensitivity TurboFold(20): 0.558 Vsfold4: 0.442 Positive Predictive Value TurboFold(20): 0.836 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 Murlet(seed): 0.457 Sensitivity TurboFold(20): 0.454 Murlet(seed): 0.253 Positive Predictive Value TurboFold(20): 0.751 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.681 Vsfold5: 0.470 Sensitivity TurboFold(20): 0.558 Vsfold5: 0.400 Positive Predictive Value TurboFold(20): 0.836 Vsfold5: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.89166989468e-09	+ TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.616 MCFold: 0.412 Sensitivity TurboFold(20): 0.512 MCFold: 0.422 Positive Predictive Value TurboFold(20): 0.747 MCFold: 0.411 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.676 RDfolder: 0.511 Sensitivity TurboFold(20): 0.541 RDfolder: 0.386 Positive Predictive Value TurboFold(20): 0.851 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.616 RNAwolf: 0.343 Sensitivity TurboFold(20): 0.508 RNAwolf: 0.325 Positive Predictive Value TurboFold(20): 0.752 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.743 CMfinder(20): 0.546 Sensitivity TurboFold(20): 0.610 CMfinder(20): 0.366 Positive Predictive Value TurboFold(20): 0.909 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.651 NanoFolder: 0.276 Sensitivity TurboFold(20): 0.531 NanoFolder: 0.286 Positive Predictive Value TurboFold(20): 0.801 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.608 TurboFold(20): 0.605 Sensitivity Multilign(seed): 0.468 TurboFold(20): 0.468 Positive Predictive Value Multilign(seed): 0.795 TurboFold(20): 0.788 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.643 PPfold(seed): 0.061 Sensitivity TurboFold(20): 0.515 PPfold(seed): 0.010 Positive Predictive Value TurboFold(20): 0.809 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.625 RSpredict(seed): 0.153 Sensitivity TurboFold(20): 0.518 RSpredict(seed): 0.060 Positive Predictive Value TurboFold(20): 0.759 RSpredict(seed): 0.402 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.600 Carnac(seed): 0.233 Sensitivity TurboFold(20): 0.473 Carnac(seed): 0.055 Positive Predictive Value TurboFold(20): 0.766 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.88760648134e-09	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.655 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.529 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.816 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MXScarna(20)	39 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 MXScarna(20): 0.617 Sensitivity CentroidAlifold(20): 0.516 MXScarna(20): 0.514 Positive Predictive Value CentroidAlifold(20): 0.879 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(seed): 0.597 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.870 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	11 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.660 MXScarna(20): 0.564 Sensitivity ContextFold: 0.525 MXScarna(20): 0.456 Positive Predictive Value ContextFold: 0.835 MXScarna(20): 0.703 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08	33 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 MXScarna(20): 0.629 Sensitivity MXScarna(seed): 0.545 MXScarna(20): 0.523 Positive Predictive Value MXScarna(seed): 0.801 MXScarna(20): 0.759 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 MXScarna(20): 0.624 Sensitivity RNAalifold(20): 0.502 MXScarna(20): 0.518 Positive Predictive Value RNAalifold(20): 0.860 MXScarna(20): 0.756 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(20): 0.530 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(20): 0.798 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	15 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.691 MXScarna(20): 0.602 Sensitivity PPfold(20): 0.544 MXScarna(20): 0.491 Positive Predictive Value PPfold(20): 0.881 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	14 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.601 MXScarna(20): 0.596 Sensitivity IPknot: 0.485 MXScarna(20): 0.483 Positive Predictive Value IPknot: 0.751 MXScarna(20): 0.741 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.115206966267	39 MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.617 CentroidAlifold(seed): 0.589 Sensitivity MXScarna(20): 0.514 CentroidAlifold(seed): 0.379 Positive Predictive Value MXScarna(20): 0.743 CentroidAlifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.624 RNASampler(20): 0.623 Sensitivity MXScarna(20): 0.518 RNASampler(20): 0.470 Positive Predictive Value MXScarna(20): 0.756 RNASampler(20): 0.830 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.925038393872	15 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.655 MXScarna(20): 0.602 Sensitivity TurboFold(20): 0.529 MXScarna(20): 0.491 Positive Predictive Value TurboFold(20): 0.816 MXScarna(20): 0.743 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.91763127434e-08		+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.624 Sfold: 0.587 Sensitivity MXScarna(20): 0.518 Sfold: 0.490 Positive Predictive Value MXScarna(20): 0.756 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 MXScarna(20): 0.629 Sensitivity CentroidHomfold‑LAST: 0.549 MXScarna(20): 0.522 Positive Predictive Value CentroidHomfold‑LAST: 0.764 MXScarna(20): 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49351211207e-07	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.624 Contrafold: 0.551 Sensitivity MXScarna(20): 0.518 Contrafold: 0.486 Positive Predictive Value MXScarna(20): 0.756 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.584 RNAalifold(seed): 0.570 Sensitivity MXScarna(20): 0.468 RNAalifold(seed): 0.351 Positive Predictive Value MXScarna(20): 0.734 RNAalifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 3.52378771889e-07	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.624 HotKnots: 0.556 Sensitivity MXScarna(20): 0.518 HotKnots: 0.495 Positive Predictive Value MXScarna(20): 0.756 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.626 MaxExpect: 0.580 Sensitivity MXScarna(20): 0.520 MaxExpect: 0.503 Positive Predictive Value MXScarna(20): 0.756 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.617 CentroidFold: 0.537 Sensitivity MXScarna(20): 0.514 CentroidFold: 0.456 Positive Predictive Value MXScarna(20): 0.743 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.624 UNAFold: 0.572 Sensitivity MXScarna(20): 0.518 UNAFold: 0.501 Positive Predictive Value MXScarna(20): 0.756 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.624 PknotsRG: 0.572 Sensitivity MXScarna(20): 0.518 PknotsRG: 0.508 Positive Predictive Value MXScarna(20): 0.756 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.623 ProbKnot: 0.578 Sensitivity MXScarna(20): 0.514 ProbKnot: 0.516 Positive Predictive Value MXScarna(20): 0.759 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Murlet(20): 0.577 Sensitivity MXScarna(20): 0.518 Murlet(20): 0.423 Positive Predictive Value MXScarna(20): 0.756 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.624 RNAfold: 0.562 Sensitivity MXScarna(20): 0.518 RNAfold: 0.497 Positive Predictive Value MXScarna(20): 0.756 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Carnac(20): 0.577 Sensitivity MXScarna(20): 0.518 Carnac(20): 0.372 Positive Predictive Value MXScarna(20): 0.756 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.624 RNAshapes: 0.567 Sensitivity MXScarna(20): 0.518 RNAshapes: 0.498 Positive Predictive Value MXScarna(20): 0.756 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.623 Fold: 0.589 Sensitivity MXScarna(20): 0.514 Fold: 0.525 Positive Predictive Value MXScarna(20): 0.759 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 MXScarna(20): 0.532 Sensitivity TurboFold(seed): 0.454 MXScarna(20): 0.422 Positive Predictive Value TurboFold(seed): 0.708 MXScarna(20): 0.675 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.615 RSpredict(20): 0.544 Sensitivity MXScarna(20): 0.514 RSpredict(20): 0.425 Positive Predictive Value MXScarna(20): 0.740 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.607 Afold: 0.530 Sensitivity MXScarna(20): 0.514 Afold: 0.478 Positive Predictive Value MXScarna(20): 0.721 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.624 RNAsubopt: 0.549 Sensitivity MXScarna(20): 0.518 RNAsubopt: 0.490 Positive Predictive Value MXScarna(20): 0.756 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.564 RNASLOpt: 0.540 Sensitivity MXScarna(20): 0.456 RNASLOpt: 0.443 Positive Predictive Value MXScarna(20): 0.703 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.79393067223e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.681 Cylofold: 0.616 Sensitivity MXScarna(20): 0.566 Cylofold: 0.528 Positive Predictive Value MXScarna(20): 0.822 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.624 McQFold: 0.539 Sensitivity MXScarna(20): 0.518 McQFold: 0.462 Positive Predictive Value MXScarna(20): 0.756 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.644 Multilign(20): 0.561 Sensitivity MXScarna(20): 0.538 Multilign(20): 0.466 Positive Predictive Value MXScarna(20): 0.777 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	? MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.569 CRWrnafold: 0.546 Sensitivity MXScarna(20): 0.466 CRWrnafold: 0.483 Positive Predictive Value MXScarna(20): 0.701 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.637 Pknots: 0.514 Sensitivity MXScarna(20): 0.530 Pknots: 0.467 Positive Predictive Value MXScarna(20): 0.769 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 MXScarna(20): 0.519 Sensitivity RNASampler(seed): 0.399 MXScarna(20): 0.423 Positive Predictive Value RNASampler(seed): 0.739 MXScarna(20): 0.641 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.724 Alterna: 0.571 Sensitivity MXScarna(20): 0.601 Alterna: 0.504 Positive Predictive Value MXScarna(20): 0.879 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Mastr(20): 0.514 Sensitivity MXScarna(20): 0.518 Mastr(20): 0.339 Positive Predictive Value MXScarna(20): 0.756 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.635 Vsfold4: 0.477 Sensitivity MXScarna(20): 0.531 Vsfold4: 0.401 Positive Predictive Value MXScarna(20): 0.764 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.599 Murlet(seed): 0.463 Sensitivity MXScarna(20): 0.479 Murlet(seed): 0.250 Positive Predictive Value MXScarna(20): 0.754 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.635 Vsfold5: 0.417 Sensitivity MXScarna(20): 0.531 Vsfold5: 0.355 Positive Predictive Value MXScarna(20): 0.764 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.616 MCFold: 0.401 Sensitivity MXScarna(20): 0.514 MCFold: 0.418 Positive Predictive Value MXScarna(20): 0.742 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.703 RDfolder: 0.541 Sensitivity MXScarna(20): 0.571 RDfolder: 0.440 Positive Predictive Value MXScarna(20): 0.871 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.590 RNAwolf: 0.348 Sensitivity MXScarna(20): 0.486 RNAwolf: 0.328 Positive Predictive Value MXScarna(20): 0.720 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.637 CMfinder(20): 0.546 Sensitivity MXScarna(20): 0.530 CMfinder(20): 0.366 Positive Predictive Value MXScarna(20): 0.770 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.594 NanoFolder: 0.276 Sensitivity MXScarna(20): 0.505 NanoFolder: 0.286 Positive Predictive Value MXScarna(20): 0.704 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.608 MXScarna(20): 0.580 Sensitivity Multilign(seed): 0.468 MXScarna(20): 0.468 Positive Predictive Value Multilign(seed): 0.795 MXScarna(20): 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.596 PPfold(seed): 0.061 Sensitivity MXScarna(20): 0.483 PPfold(seed): 0.010 Positive Predictive Value MXScarna(20): 0.741 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.615 RSpredict(seed): 0.191 Sensitivity MXScarna(20): 0.514 RSpredict(seed): 0.079 Positive Predictive Value MXScarna(20): 0.740 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.612 Carnac(seed): 0.186 Sensitivity MXScarna(20): 0.505 Carnac(seed): 0.035 Positive Predictive Value MXScarna(20): 0.746 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.624 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.756 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 MXScarna(20): 0.741 Sensitivity PETfold_2.0(seed): 0.614 MXScarna(20): 0.614 Positive Predictive Value PETfold_2.0(seed): 0.946 MXScarna(20): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 0.741 PETfold_2.0(20): 0.647 Sensitivity MXScarna(20): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value MXScarna(20): 0.897 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Sfold	39 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Sfold: 0.558 Sensitivity CentroidAlifold(20): 0.516 Sfold: 0.468 Positive Predictive Value CentroidAlifold(20): 0.879 Sfold: 0.669 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Sfold: 0.505 Sensitivity PETfold_pre2.0(seed): 0.602 Sfold: 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Sfold: 0.601 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.563 Sfold: 0.493 Sensitivity ContextFold: 0.466 Sfold: 0.418 Positive Predictive Value ContextFold: 0.681 Sfold: 0.583 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.667 Sfold: 0.570 Sensitivity MXScarna(seed): 0.560 Sfold: 0.490 Positive Predictive Value MXScarna(seed): 0.794 Sfold: 0.665 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.656 Sfold: 0.587 Sensitivity RNAalifold(20): 0.502 Sfold: 0.490 Positive Predictive Value RNAalifold(20): 0.860 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Sfold: 0.500 Sensitivity PETfold_pre2.0(20): 0.530 Sfold: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	15 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.691 Sfold: 0.594 Sensitivity PPfold(20): 0.544 Sfold: 0.488 Positive Predictive Value PPfold(20): 0.881 Sfold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	57 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.554 Sfold: 0.504 Sensitivity IPknot: 0.448 Sfold: 0.427 Positive Predictive Value IPknot: 0.688 Sfold: 0.596 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 Sfold: 0.562 Sensitivity CentroidAlifold(seed): 0.443 Sfold: 0.482 Positive Predictive Value CentroidAlifold(seed): 0.880 Sfold: 0.657 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.623 Sfold: 0.587 Sensitivity RNASampler(20): 0.470 Sfold: 0.490 Positive Predictive Value RNASampler(20): 0.830 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.655 Sfold: 0.594 Sensitivity TurboFold(20): 0.529 Sfold: 0.488 Positive Predictive Value TurboFold(20): 0.816 Sfold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.91763127434e-08	34 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.624 Sfold: 0.587 Sensitivity MXScarna(20): 0.518 Sfold: 0.490 Positive Predictive Value MXScarna(20): 0.756 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.614 CentroidHomfold‑LAST: 0.587 Sensitivity Sfold: 0.516 CentroidHomfold‑LAST: 0.439 Positive Predictive Value Sfold: 0.735 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 1.5875416339e-07	- Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.542 Sfold: 0.508 Sensitivity Contrafold: 0.477 Sfold: 0.432 Positive Predictive Value Contrafold: 0.616 Sfold: 0.599 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.631 Sfold: 0.566 Sensitivity RNAalifold(seed): 0.460 Sfold: 0.485 Positive Predictive Value RNAalifold(seed): 0.866 Sfold: 0.661 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.640 HotKnots: 0.622 Sensitivity Sfold: 0.548 HotKnots: 0.558 Positive Predictive Value Sfold: 0.751 HotKnots: 0.699 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.552 Sfold: 0.544 Sensitivity MaxExpect: 0.480 Sfold: 0.460 Positive Predictive Value MaxExpect: 0.635 Sfold: 0.645 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.000150377120024	- CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.529 Sfold: 0.520 Sensitivity CentroidFold: 0.442 Sfold: 0.443 Positive Predictive Value CentroidFold: 0.634 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.508 UNAFold: 0.489 Sensitivity Sfold: 0.432 UNAFold: 0.434 Positive Predictive Value Sfold: 0.599 UNAFold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.511 PknotsRG: 0.478 Sensitivity Sfold: 0.433 PknotsRG: 0.430 Positive Predictive Value Sfold: 0.604 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.557 ProbKnot: 0.536 Sensitivity Sfold: 0.480 ProbKnot: 0.480 Positive Predictive Value Sfold: 0.649 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.587 Murlet(20): 0.577 Sensitivity Sfold: 0.490 Murlet(20): 0.423 Positive Predictive Value Sfold: 0.708 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.34513818976e-06	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.508 RNAfold: 0.484 Sensitivity Sfold: 0.432 RNAfold: 0.434 Positive Predictive Value Sfold: 0.599 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.587 Carnac(20): 0.577 Sensitivity Sfold: 0.490 Carnac(20): 0.372 Positive Predictive Value Sfold: 0.708 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.640 RNAshapes: 0.602 Sensitivity Sfold: 0.548 RNAshapes: 0.533 Positive Predictive Value Sfold: 0.751 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.570 Fold: 0.535 Sensitivity Sfold: 0.491 Fold: 0.481 Positive Predictive Value Sfold: 0.662 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.559 TurboFold(seed): 0.544 Sensitivity Sfold: 0.439 TurboFold(seed): 0.439 Positive Predictive Value Sfold: 0.718 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.50659327008e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.563 RSpredict(20): 0.544 Sensitivity Sfold: 0.476 RSpredict(20): 0.425 Positive Predictive Value Sfold: 0.671 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.492 Afold: 0.468 Sensitivity Sfold: 0.419 Afold: 0.425 Positive Predictive Value Sfold: 0.577 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.640 RNAsubopt: 0.595 Sensitivity Sfold: 0.548 RNAsubopt: 0.534 Positive Predictive Value Sfold: 0.751 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.575 RNASLOpt: 0.489 Sensitivity Sfold: 0.478 RNASLOpt: 0.393 Positive Predictive Value Sfold: 0.696 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.607 Sensitivity Sfold: 0.563 Cylofold: 0.517 Positive Predictive Value Sfold: 0.772 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.508 McQFold: 0.415 Sensitivity Sfold: 0.431 McQFold: 0.332 Positive Predictive Value Sfold: 0.598 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.598 Multilign(20): 0.561 Sensitivity Sfold: 0.501 Multilign(20): 0.466 Positive Predictive Value Sfold: 0.720 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.618 CRWrnafold: 0.585 Sensitivity Sfold: 0.530 CRWrnafold: 0.522 Positive Predictive Value Sfold: 0.728 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.673 Pknots: 0.601 Sensitivity Sfold: 0.579 Pknots: 0.545 Positive Predictive Value Sfold: 0.787 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.678 RNASampler(seed): 0.635 Sensitivity Sfold: 0.588 RNASampler(seed): 0.484 Positive Predictive Value Sfold: 0.785 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.719 Alterna: 0.665 Sensitivity Sfold: 0.625 Alterna: 0.599 Positive Predictive Value Sfold: 0.833 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.587 Mastr(20): 0.514 Sensitivity Sfold: 0.490 Mastr(20): 0.339 Positive Predictive Value Sfold: 0.708 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.652 Vsfold4: 0.547 Sensitivity Sfold: 0.564 Vsfold4: 0.465 Positive Predictive Value Sfold: 0.759 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.656 Murlet(seed): 0.514 Sensitivity Sfold: 0.549 Murlet(seed): 0.315 Positive Predictive Value Sfold: 0.788 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.647 Vsfold5: 0.510 Sensitivity Sfold: 0.558 Vsfold5: 0.441 Positive Predictive Value Sfold: 0.755 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.663 MCFold: 0.522 Sensitivity Sfold: 0.574 MCFold: 0.535 Positive Predictive Value Sfold: 0.771 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.709 RDfolder: 0.592 Sensitivity Sfold: 0.616 RDfolder: 0.491 Positive Predictive Value Sfold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.506 RNAwolf: 0.356 Sensitivity Sfold: 0.428 RNAwolf: 0.331 Positive Predictive Value Sfold: 0.598 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.618 CMfinder(20): 0.546 Sensitivity Sfold: 0.524 CMfinder(20): 0.366 Positive Predictive Value Sfold: 0.735 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.579 NanoFolder: 0.339 Sensitivity Sfold: 0.493 NanoFolder: 0.350 Positive Predictive Value Sfold: 0.684 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.584 Multilign(seed): 0.558 Sensitivity Sfold: 0.462 Multilign(seed): 0.434 Positive Predictive Value Sfold: 0.746 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.558 PPfold(seed): 0.092 Sensitivity Sfold: 0.449 PPfold(seed): 0.016 Positive Predictive Value Sfold: 0.699 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.565 RSpredict(seed): 0.375 Sensitivity Sfold: 0.486 RSpredict(seed): 0.220 Positive Predictive Value Sfold: 0.657 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.593 Carnac(seed): 0.404 Sensitivity Sfold: 0.508 Carnac(seed): 0.181 Positive Predictive Value Sfold: 0.695 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.601 Mastr(seed): 0.236 Sensitivity Sfold: 0.513 Mastr(seed): 0.062 Positive Predictive Value Sfold: 0.707 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Sfold: 0.673 Sensitivity PETfold_2.0(seed): 0.642 Sfold: 0.537 Positive Predictive Value PETfold_2.0(seed): 0.924 Sfold: 0.850 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Sfold: 0.514 Sensitivity PETfold_2.0(20): 0.509 Sfold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidHomfold‑LAST	21 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.683 CentroidHomfold‑LAST: 0.594 Sensitivity CentroidAlifold(20): 0.533 CentroidHomfold‑LAST: 0.501 Positive Predictive Value CentroidAlifold(20): 0.880 CentroidHomfold‑LAST: 0.709 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.574 Sensitivity PETfold_pre2.0(seed): 0.606 CentroidHomfold‑LAST: 0.489 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CentroidHomfold‑LAST: 0.680 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	41 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.662 CentroidHomfold‑LAST: 0.559 Sensitivity ContextFold: 0.547 CentroidHomfold‑LAST: 0.417 Positive Predictive Value ContextFold: 0.806 CentroidHomfold‑LAST: 0.753 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.645 CentroidHomfold‑LAST: 0.626 Sensitivity MXScarna(seed): 0.530 CentroidHomfold‑LAST: 0.534 Positive Predictive Value MXScarna(seed): 0.792 CentroidHomfold‑LAST: 0.740 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.00960443857e-07	14 RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.685 CentroidHomfold‑LAST: 0.645 Sensitivity RNAalifold(20): 0.541 CentroidHomfold‑LAST: 0.549 Positive Predictive Value RNAalifold(20): 0.872 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	17 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 CentroidHomfold‑LAST: 0.565 Sensitivity PETfold_pre2.0(20): 0.559 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(20): 0.826 CentroidHomfold‑LAST: 0.668 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.22210847902e-08	14 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.723 CentroidHomfold‑LAST: 0.645 Sensitivity PPfold(20): 0.581 CentroidHomfold‑LAST: 0.549 Positive Predictive Value PPfold(20): 0.905 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	49 IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.635 CentroidHomfold‑LAST: 0.583 Sensitivity IPknot: 0.531 CentroidHomfold‑LAST: 0.437 Positive Predictive Value IPknot: 0.761 CentroidHomfold‑LAST: 0.781 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 CentroidAlifold(seed): 0.563 Sensitivity CentroidHomfold‑LAST: 0.503 CentroidAlifold(seed): 0.345 Positive Predictive Value CentroidHomfold‑LAST: 0.711 CentroidAlifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.659 CentroidHomfold‑LAST: 0.645 Sensitivity RNASampler(20): 0.507 CentroidHomfold‑LAST: 0.549 Positive Predictive Value RNASampler(20): 0.861 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.53530931377e-06	14 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.681 CentroidHomfold‑LAST: 0.645 Sensitivity TurboFold(20): 0.558 CentroidHomfold‑LAST: 0.549 Positive Predictive Value TurboFold(20): 0.836 CentroidHomfold‑LAST: 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.39551335374e-08	14 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 MXScarna(20): 0.629 Sensitivity CentroidHomfold‑LAST: 0.549 MXScarna(20): 0.522 Positive Predictive Value CentroidHomfold‑LAST: 0.764 MXScarna(20): 0.764 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49351211207e-07	56 Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.614 CentroidHomfold‑LAST: 0.587 Sensitivity Sfold: 0.516 CentroidHomfold‑LAST: 0.439 Positive Predictive Value Sfold: 0.735 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 1.5875416339e-07		= Contrafold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Contrafold: 0.594 CentroidHomfold‑LAST: 0.587 Sensitivity Contrafold: 0.514 CentroidHomfold‑LAST: 0.439 Positive Predictive Value Contrafold: 0.690 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.00324372766907	- RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.584 CentroidHomfold‑LAST: 0.556 Sensitivity RNAalifold(seed): 0.398 CentroidHomfold‑LAST: 0.472 Positive Predictive Value RNAalifold(seed): 0.865 CentroidHomfold‑LAST: 0.663 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.68555027914e-06	- HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.600 CentroidHomfold‑LAST: 0.587 Sensitivity HotKnots: 0.525 CentroidHomfold‑LAST: 0.439 Positive Predictive Value HotKnots: 0.691 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 2.28033735003e-07	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 MaxExpect: 0.563 Sensitivity CentroidHomfold‑LAST: 0.439 MaxExpect: 0.486 Positive Predictive Value CentroidHomfold‑LAST: 0.789 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.578 CentroidFold: 0.548 Sensitivity CentroidHomfold‑LAST: 0.440 CentroidFold: 0.458 Positive Predictive Value CentroidHomfold‑LAST: 0.763 CentroidFold: 0.661 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 UNAFold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.439 UNAFold: 0.501 Positive Predictive Value CentroidHomfold‑LAST: 0.789 UNAFold: 0.665 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 2.38297003775e-06	= CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 PknotsRG: 0.582 Sensitivity CentroidHomfold‑LAST: 0.439 PknotsRG: 0.509 Positive Predictive Value CentroidHomfold‑LAST: 0.789 PknotsRG: 0.670 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.0955699217783	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 ProbKnot: 0.562 Sensitivity CentroidHomfold‑LAST: 0.439 ProbKnot: 0.497 Positive Predictive Value CentroidHomfold‑LAST: 0.789 ProbKnot: 0.641 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Murlet(20): 0.590 Sensitivity CentroidHomfold‑LAST: 0.549 Murlet(20): 0.453 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Murlet(20): 0.774 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	= CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAfold: 0.585 Sensitivity CentroidHomfold‑LAST: 0.439 RNAfold: 0.508 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAfold: 0.677 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.647668092439	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Carnac(20): 0.568 Sensitivity CentroidHomfold‑LAST: 0.549 Carnac(20): 0.382 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Carnac(20): 0.850 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAshapes: 0.558 Sensitivity CentroidHomfold‑LAST: 0.439 RNAshapes: 0.483 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAshapes: 0.650 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 Fold: 0.537 Sensitivity CentroidHomfold‑LAST: 0.439 Fold: 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.789 Fold: 0.615 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.566 CentroidHomfold‑LAST: 0.556 Sensitivity TurboFold(seed): 0.467 CentroidHomfold‑LAST: 0.461 Positive Predictive Value TurboFold(seed): 0.693 CentroidHomfold‑LAST: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.63118549175e-06	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 RSpredict(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.512 RSpredict(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.708 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	= CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.595 Afold: 0.585 Sensitivity CentroidHomfold‑LAST: 0.454 Afold: 0.527 Positive Predictive Value CentroidHomfold‑LAST: 0.786 Afold: 0.655 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.00842627253913	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAsubopt: 0.561 Sensitivity CentroidHomfold‑LAST: 0.439 RNAsubopt: 0.493 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAsubopt: 0.642 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.559 RNASLOpt: 0.512 Sensitivity CentroidHomfold‑LAST: 0.417 RNASLOpt: 0.409 Positive Predictive Value CentroidHomfold‑LAST: 0.753 RNASLOpt: 0.646 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.591 Cylofold: 0.534 Sensitivity CentroidHomfold‑LAST: 0.451 Cylofold: 0.448 Positive Predictive Value CentroidHomfold‑LAST: 0.781 Cylofold: 0.645 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 McQFold: 0.538 Sensitivity CentroidHomfold‑LAST: 0.439 McQFold: 0.453 Positive Predictive Value CentroidHomfold‑LAST: 0.789 McQFold: 0.644 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Multilign(20): 0.596 Sensitivity CentroidHomfold‑LAST: 0.549 Multilign(20): 0.507 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 CRWrnafold: 0.576 Sensitivity CentroidHomfold‑LAST: 0.501 CRWrnafold: 0.513 Positive Predictive Value CentroidHomfold‑LAST: 0.845 CRWrnafold: 0.654 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.661 Pknots: 0.571 Sensitivity CentroidHomfold‑LAST: 0.538 Pknots: 0.506 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Pknots: 0.652 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.574 RNASampler(seed): 0.509 Sensitivity CentroidHomfold‑LAST: 0.471 RNASampler(seed): 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.706 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Alterna: 0.608 Sensitivity CentroidHomfold‑LAST: 0.533 Alterna: 0.544 Positive Predictive Value CentroidHomfold‑LAST: 0.915 Alterna: 0.690 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Mastr(20): 0.566 Sensitivity CentroidHomfold‑LAST: 0.549 Mastr(20): 0.409 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.624 Vsfold4: 0.516 Sensitivity CentroidHomfold‑LAST: 0.484 Vsfold4: 0.430 Positive Predictive Value CentroidHomfold‑LAST: 0.811 Vsfold4: 0.626 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.556 Murlet(seed): 0.441 Sensitivity CentroidHomfold‑LAST: 0.472 Murlet(seed): 0.267 Positive Predictive Value CentroidHomfold‑LAST: 0.663 Murlet(seed): 0.738 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 Vsfold5: 0.452 Sensitivity CentroidHomfold‑LAST: 0.469 Vsfold5: 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.775 Vsfold5: 0.533 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.622 MCFold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.510 MCFold: 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.765 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.694 RDfolder: 0.534 Sensitivity CentroidHomfold‑LAST: 0.550 RDfolder: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.883 RDfolder: 0.684 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.574 RNAwolf: 0.400 Sensitivity CentroidHomfold‑LAST: 0.439 RNAwolf: 0.372 Positive Predictive Value CentroidHomfold‑LAST: 0.755 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.591 CMfinder(20): 0.546 Sensitivity CentroidHomfold‑LAST: 0.543 CMfinder(20): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.650 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.623 NanoFolder: 0.323 Sensitivity CentroidHomfold‑LAST: 0.497 NanoFolder: 0.333 Positive Predictive Value CentroidHomfold‑LAST: 0.787 NanoFolder: 0.322 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.612 Multilign(seed): 0.590 Sensitivity CentroidHomfold‑LAST: 0.509 Multilign(seed): 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.744 Multilign(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.616 PPfold(seed): 0.077 Sensitivity CentroidHomfold‑LAST: 0.523 PPfold(seed): 0.011 Positive Predictive Value CentroidHomfold‑LAST: 0.731 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 RSpredict(seed): 0.147 Sensitivity CentroidHomfold‑LAST: 0.512 RSpredict(seed): 0.061 Positive Predictive Value CentroidHomfold‑LAST: 0.710 RSpredict(seed): 0.362 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.572 Carnac(seed): 0.242 Sensitivity CentroidHomfold‑LAST: 0.483 Carnac(seed): 0.059 Positive Predictive Value CentroidHomfold‑LAST: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.16590079822e-09	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.626 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.534 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.740 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	? CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(seed): 0.614 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(20): 0.509 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Contrafold	39 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Contrafold: 0.534 Sensitivity CentroidAlifold(20): 0.516 Contrafold: 0.474 Positive Predictive Value CentroidAlifold(20): 0.879 Contrafold: 0.607 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Contrafold: 0.565 Sensitivity PETfold_pre2.0(seed): 0.602 Contrafold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Contrafold: 0.650 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	49 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.563 Contrafold: 0.487 Sensitivity ContextFold: 0.466 Contrafold: 0.419 Positive Predictive Value ContextFold: 0.681 Contrafold: 0.568 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.667 Contrafold: 0.599 Sensitivity MXScarna(seed): 0.560 Contrafold: 0.535 Positive Predictive Value MXScarna(seed): 0.794 Contrafold: 0.671 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.656 Contrafold: 0.551 Sensitivity RNAalifold(20): 0.502 Contrafold: 0.486 Positive Predictive Value RNAalifold(20): 0.860 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Contrafold: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.798 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	15 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.691 Contrafold: 0.588 Sensitivity PPfold(20): 0.544 Contrafold: 0.507 Positive Predictive Value PPfold(20): 0.881 Contrafold: 0.687 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	57 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.554 Contrafold: 0.500 Sensitivity IPknot: 0.448 Contrafold: 0.430 Positive Predictive Value IPknot: 0.688 Contrafold: 0.582 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 Contrafold: 0.586 Sensitivity CentroidAlifold(seed): 0.443 Contrafold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.880 Contrafold: 0.658 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.48494289621e-08	34 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.623 Contrafold: 0.551 Sensitivity RNASampler(20): 0.470 Contrafold: 0.486 Positive Predictive Value RNASampler(20): 0.830 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.655 Contrafold: 0.588 Sensitivity TurboFold(20): 0.529 Contrafold: 0.507 Positive Predictive Value TurboFold(20): 0.816 Contrafold: 0.687 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	34 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.624 Contrafold: 0.551 Sensitivity MXScarna(20): 0.518 Contrafold: 0.486 Positive Predictive Value MXScarna(20): 0.756 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.542 Sfold: 0.508 Sensitivity Contrafold: 0.477 Sfold: 0.432 Positive Predictive Value Contrafold: 0.616 Sfold: 0.599 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 Contrafold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Contrafold: 0.594 CentroidHomfold‑LAST: 0.587 Sensitivity Contrafold: 0.514 CentroidHomfold‑LAST: 0.439 Positive Predictive Value Contrafold: 0.690 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.00324372766907		- RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.631 Contrafold: 0.598 Sensitivity RNAalifold(seed): 0.460 Contrafold: 0.532 Positive Predictive Value RNAalifold(seed): 0.866 Contrafold: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08	= HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.622 Contrafold: 0.618 Sensitivity HotKnots: 0.558 Contrafold: 0.550 Positive Predictive Value HotKnots: 0.699 Contrafold: 0.700 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00985919189012	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.561 MaxExpect: 0.552 Sensitivity Contrafold: 0.489 MaxExpect: 0.480 Positive Predictive Value Contrafold: 0.644 MaxExpect: 0.635 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ Contrafold vs CentroidFold Matthews Correlation Coefficient Contrafold: 0.532 CentroidFold: 0.529 Sensitivity Contrafold: 0.472 CentroidFold: 0.442 Positive Predictive Value Contrafold: 0.601 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 9.94962292175e-07	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.542 UNAFold: 0.489 Sensitivity Contrafold: 0.477 UNAFold: 0.434 Positive Predictive Value Contrafold: 0.616 UNAFold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.539 PknotsRG: 0.478 Sensitivity Contrafold: 0.475 PknotsRG: 0.430 Positive Predictive Value Contrafold: 0.613 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.547 ProbKnot: 0.536 Sensitivity Contrafold: 0.482 ProbKnot: 0.480 Positive Predictive Value Contrafold: 0.623 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 1.27481660653e-07	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.577 Contrafold: 0.551 Sensitivity Murlet(20): 0.423 Contrafold: 0.486 Positive Predictive Value Murlet(20): 0.791 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.542 RNAfold: 0.484 Sensitivity Contrafold: 0.477 RNAfold: 0.434 Positive Predictive Value Contrafold: 0.616 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.577 Contrafold: 0.551 Sensitivity Carnac(20): 0.372 Contrafold: 0.486 Positive Predictive Value Carnac(20): 0.897 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.618 RNAshapes: 0.602 Sensitivity Contrafold: 0.550 RNAshapes: 0.533 Positive Predictive Value Contrafold: 0.700 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.563 Fold: 0.535 Sensitivity Contrafold: 0.496 Fold: 0.481 Positive Predictive Value Contrafold: 0.640 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	= TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.544 Contrafold: 0.544 Sensitivity TurboFold(seed): 0.439 Contrafold: 0.456 Positive Predictive Value TurboFold(seed): 0.679 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0195049618507	- RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.544 Contrafold: 0.539 Sensitivity RSpredict(20): 0.425 Contrafold: 0.480 Positive Predictive Value RSpredict(20): 0.701 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000332169954379	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.534 Afold: 0.468 Sensitivity Contrafold: 0.473 Afold: 0.425 Positive Predictive Value Contrafold: 0.603 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.618 RNAsubopt: 0.595 Sensitivity Contrafold: 0.550 RNAsubopt: 0.534 Positive Predictive Value Contrafold: 0.700 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.548 RNASLOpt: 0.489 Sensitivity Contrafold: 0.474 RNASLOpt: 0.393 Positive Predictive Value Contrafold: 0.637 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.672 Cylofold: 0.607 Sensitivity Contrafold: 0.597 Cylofold: 0.517 Positive Predictive Value Contrafold: 0.761 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.541 McQFold: 0.415 Sensitivity Contrafold: 0.476 McQFold: 0.332 Positive Predictive Value Contrafold: 0.616 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.576 Multilign(20): 0.561 Sensitivity Contrafold: 0.505 Multilign(20): 0.466 Positive Predictive Value Contrafold: 0.663 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.99999654892e-06	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.636 CRWrnafold: 0.585 Sensitivity Contrafold: 0.559 CRWrnafold: 0.522 Positive Predictive Value Contrafold: 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.657 Pknots: 0.601 Sensitivity Contrafold: 0.585 Pknots: 0.545 Positive Predictive Value Contrafold: 0.743 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.671 RNASampler(seed): 0.635 Sensitivity Contrafold: 0.603 RNASampler(seed): 0.484 Positive Predictive Value Contrafold: 0.751 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.730 Alterna: 0.665 Sensitivity Contrafold: 0.648 Alterna: 0.599 Positive Predictive Value Contrafold: 0.829 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.551 Mastr(20): 0.514 Sensitivity Contrafold: 0.486 Mastr(20): 0.339 Positive Predictive Value Contrafold: 0.630 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.642 Vsfold4: 0.547 Sensitivity Contrafold: 0.574 Vsfold4: 0.465 Positive Predictive Value Contrafold: 0.722 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.647 Murlet(seed): 0.514 Sensitivity Contrafold: 0.569 Murlet(seed): 0.315 Positive Predictive Value Contrafold: 0.741 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.648 Vsfold5: 0.510 Sensitivity Contrafold: 0.580 Vsfold5: 0.441 Positive Predictive Value Contrafold: 0.730 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.634 MCFold: 0.522 Sensitivity Contrafold: 0.568 MCFold: 0.535 Positive Predictive Value Contrafold: 0.713 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.724 RDfolder: 0.592 Sensitivity Contrafold: 0.643 RDfolder: 0.491 Positive Predictive Value Contrafold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.500 RNAwolf: 0.356 Sensitivity Contrafold: 0.432 RNAwolf: 0.331 Positive Predictive Value Contrafold: 0.579 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.614 CMfinder(20): 0.546 Sensitivity Contrafold: 0.543 CMfinder(20): 0.366 Positive Predictive Value Contrafold: 0.701 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.574 NanoFolder: 0.339 Sensitivity Contrafold: 0.505 NanoFolder: 0.350 Positive Predictive Value Contrafold: 0.658 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.602 Multilign(seed): 0.558 Sensitivity Contrafold: 0.500 Multilign(seed): 0.434 Positive Predictive Value Contrafold: 0.730 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.595 PPfold(seed): 0.092 Sensitivity Contrafold: 0.507 PPfold(seed): 0.016 Positive Predictive Value Contrafold: 0.703 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.589 RSpredict(seed): 0.375 Sensitivity Contrafold: 0.528 RSpredict(seed): 0.220 Positive Predictive Value Contrafold: 0.660 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.621 Carnac(seed): 0.404 Sensitivity Contrafold: 0.548 Carnac(seed): 0.181 Positive Predictive Value Contrafold: 0.704 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.596 Mastr(seed): 0.236 Sensitivity Contrafold: 0.536 Mastr(seed): 0.062 Positive Predictive Value Contrafold: 0.668 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Contrafold: 0.649 Sensitivity PETfold_2.0(seed): 0.642 Contrafold: 0.547 Positive Predictive Value PETfold_2.0(seed): 0.924 Contrafold: 0.776 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Contrafold: 0.482 Sensitivity PETfold_2.0(20): 0.509 Contrafold: 0.386 Positive Predictive Value PETfold_2.0(20): 0.829 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAalifold(seed)	21 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.601 RNAalifold(seed): 0.557 Sensitivity CentroidAlifold(20): 0.416 RNAalifold(seed): 0.334 Positive Predictive Value CentroidAlifold(20): 0.871 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	14 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAalifold(seed): 0.637 Sensitivity PETfold_pre2.0(seed): 0.570 RNAalifold(seed): 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.811 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	10 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.665 RNAalifold(seed): 0.652 Sensitivity ContextFold: 0.549 RNAalifold(seed): 0.506 Positive Predictive Value ContextFold: 0.808 RNAalifold(seed): 0.839 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.28582059552e-06	34 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.643 RNAalifold(seed): 0.631 Sensitivity MXScarna(seed): 0.536 RNAalifold(seed): 0.460 Positive Predictive Value MXScarna(seed): 0.773 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.62644058675e-08	20 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.578 RNAalifold(seed): 0.570 Sensitivity RNAalifold(20): 0.414 RNAalifold(seed): 0.351 Positive Predictive Value RNAalifold(20): 0.809 RNAalifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.000112898315885	8 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.527 PETfold_pre2.0(20): 0.449 Sensitivity RNAalifold(seed): 0.278 PETfold_pre2.0(20): 0.342 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.581 PPfold(20): 0.576 Sensitivity RNAalifold(seed): 0.362 PPfold(20): 0.423 Positive Predictive Value RNAalifold(seed): 0.938 PPfold(20): 0.790 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.648 IPknot: 0.596 Sensitivity RNAalifold(seed): 0.501 IPknot: 0.491 Positive Predictive Value RNAalifold(seed): 0.839 IPknot: 0.725 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.11186924993e-07	37 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.675 RNAalifold(seed): 0.625 Sensitivity CentroidAlifold(seed): 0.525 RNAalifold(seed): 0.449 Positive Predictive Value CentroidAlifold(seed): 0.870 RNAalifold(seed): 0.871 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 RNASampler(20): 0.563 Sensitivity RNAalifold(seed): 0.351 RNASampler(20): 0.411 Positive Predictive Value RNAalifold(seed): 0.930 RNASampler(20): 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.23133840878e-05	9 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 RNAalifold(seed): 0.581 Sensitivity TurboFold(20): 0.454 RNAalifold(seed): 0.362 Positive Predictive Value TurboFold(20): 0.751 RNAalifold(seed): 0.938 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	20 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.584 RNAalifold(seed): 0.570 Sensitivity MXScarna(20): 0.468 RNAalifold(seed): 0.351 Positive Predictive Value MXScarna(20): 0.734 RNAalifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 3.52378771889e-07	34 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.631 Sfold: 0.566 Sensitivity RNAalifold(seed): 0.460 Sfold: 0.485 Positive Predictive Value RNAalifold(seed): 0.866 Sfold: 0.661 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08	11 RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.584 CentroidHomfold‑LAST: 0.556 Sensitivity RNAalifold(seed): 0.398 CentroidHomfold‑LAST: 0.472 Positive Predictive Value RNAalifold(seed): 0.865 CentroidHomfold‑LAST: 0.663 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.68555027914e-06	34 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.631 Contrafold: 0.598 Sensitivity RNAalifold(seed): 0.460 Contrafold: 0.532 Positive Predictive Value RNAalifold(seed): 0.866 Contrafold: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08		+ RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.596 HotKnots: 0.579 Sensitivity RNAalifold(seed): 0.397 HotKnots: 0.532 Positive Predictive Value RNAalifold(seed): 0.897 HotKnots: 0.635 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.630 MaxExpect: 0.548 Sensitivity RNAalifold(seed): 0.460 MaxExpect: 0.485 Positive Predictive Value RNAalifold(seed): 0.863 MaxExpect: 0.621 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.625 CentroidFold: 0.585 Sensitivity RNAalifold(seed): 0.449 CentroidFold: 0.499 Positive Predictive Value RNAalifold(seed): 0.871 CentroidFold: 0.686 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 UNAFold: 0.541 Sensitivity RNAalifold(seed): 0.460 UNAFold: 0.483 Positive Predictive Value RNAalifold(seed): 0.866 UNAFold: 0.608 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.596 PknotsRG: 0.593 Sensitivity RNAalifold(seed): 0.397 PknotsRG: 0.542 Positive Predictive Value RNAalifold(seed): 0.897 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.178906439528	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.606 ProbKnot: 0.511 Sensitivity RNAalifold(seed): 0.435 ProbKnot: 0.459 Positive Predictive Value RNAalifold(seed): 0.845 ProbKnot: 0.571 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Murlet(20): 0.497 Sensitivity RNAalifold(seed): 0.351 Murlet(20): 0.340 Positive Predictive Value RNAalifold(seed): 0.930 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.631 RNAfold: 0.549 Sensitivity RNAalifold(seed): 0.460 RNAfold: 0.493 Positive Predictive Value RNAalifold(seed): 0.866 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Carnac(20): 0.507 Sensitivity RNAalifold(seed): 0.351 Carnac(20): 0.275 Positive Predictive Value RNAalifold(seed): 0.930 Carnac(20): 0.939 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.596 RNAshapes: 0.595 Sensitivity RNAalifold(seed): 0.397 RNAshapes: 0.537 Positive Predictive Value RNAalifold(seed): 0.897 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 9.17559933998e-05	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.626 Fold: 0.520 Sensitivity RNAalifold(seed): 0.457 Fold: 0.472 Positive Predictive Value RNAalifold(seed): 0.857 Fold: 0.573 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	= RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.532 TurboFold(seed): 0.518 Sensitivity RNAalifold(seed): 0.341 TurboFold(seed): 0.416 Positive Predictive Value RNAalifold(seed): 0.837 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0168018190577	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.556 RSpredict(20): 0.435 Sensitivity RNAalifold(seed): 0.333 RSpredict(20): 0.328 Positive Predictive Value RNAalifold(seed): 0.932 RSpredict(20): 0.583 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.602 RNAalifold(seed): 0.576 Sensitivity Afold: 0.565 RNAalifold(seed): 0.383 Positive Predictive Value Afold: 0.646 RNAalifold(seed): 0.867 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.596 RNAsubopt: 0.569 Sensitivity RNAalifold(seed): 0.397 RNAsubopt: 0.521 Positive Predictive Value RNAalifold(seed): 0.897 RNAsubopt: 0.625 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.552 RNASLOpt: 0.426 Sensitivity RNAalifold(seed): 0.348 RNASLOpt: 0.352 Positive Predictive Value RNAalifold(seed): 0.879 RNASLOpt: 0.523 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.592 RNAalifold(seed): 0.589 Sensitivity Cylofold: 0.506 RNAalifold(seed): 0.398 Positive Predictive Value Cylofold: 0.700 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.068096332007	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 McQFold: 0.536 Sensitivity RNAalifold(seed): 0.460 McQFold: 0.469 Positive Predictive Value RNAalifold(seed): 0.866 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 Multilign(20): 0.431 Sensitivity RNAalifold(seed): 0.375 Multilign(20): 0.346 Positive Predictive Value RNAalifold(seed): 0.938 Multilign(20): 0.544 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.500 CRWrnafold: 0.419 Sensitivity RNAalifold(seed): 0.320 CRWrnafold: 0.377 Positive Predictive Value RNAalifold(seed): 0.789 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.633 Pknots: 0.595 Sensitivity RNAalifold(seed): 0.440 Pknots: 0.548 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.651 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.62644058675e-08	- RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 RNAalifold(seed): 0.629 Sensitivity RNASampler(seed): 0.484 RNAalifold(seed): 0.451 Positive Predictive Value RNASampler(seed): 0.837 RNAalifold(seed): 0.881 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30966813656e-06	- Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.763 RNAalifold(seed): 0.672 Sensitivity Alterna: 0.683 RNAalifold(seed): 0.524 Positive Predictive Value Alterna: 0.858 RNAalifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Mastr(20): 0.393 Sensitivity RNAalifold(seed): 0.351 Mastr(20): 0.198 Positive Predictive Value RNAalifold(seed): 0.930 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.600 Vsfold4: 0.506 Sensitivity RNAalifold(seed): 0.403 Vsfold4: 0.439 Positive Predictive Value RNAalifold(seed): 0.895 Vsfold4: 0.589 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.639 Murlet(seed): 0.514 Sensitivity RNAalifold(seed): 0.449 Murlet(seed): 0.315 Positive Predictive Value RNAalifold(seed): 0.914 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.603 Vsfold5: 0.483 Sensitivity RNAalifold(seed): 0.407 Vsfold5: 0.422 Positive Predictive Value RNAalifold(seed): 0.895 Vsfold5: 0.558 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.608 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.408 MCFold: 0.492 Positive Predictive Value RNAalifold(seed): 0.909 MCFold: 0.467 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.668 RDfolder: 0.580 Sensitivity RNAalifold(seed): 0.505 RDfolder: 0.474 Positive Predictive Value RNAalifold(seed): 0.891 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNAwolf: 0.408 Sensitivity RNAalifold(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value RNAalifold(seed): 0.849 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.76499031155e-08	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.727 CMfinder(20): 0.466 Sensitivity RNAalifold(seed): 0.531 CMfinder(20): 0.219 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.516 NanoFolder: 0.252 Sensitivity RNAalifold(seed): 0.331 NanoFolder: 0.266 Positive Predictive Value RNAalifold(seed): 0.810 NanoFolder: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.563 Multilign(seed): 0.558 Sensitivity RNAalifold(seed): 0.381 Multilign(seed): 0.434 Positive Predictive Value RNAalifold(seed): 0.838 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.563 PPfold(seed): 0.124 Sensitivity RNAalifold(seed): 0.366 PPfold(seed): 0.030 Positive Predictive Value RNAalifold(seed): 0.871 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.21732636221e-09	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.624 RSpredict(seed): 0.464 Sensitivity RNAalifold(seed): 0.448 RSpredict(seed): 0.306 Positive Predictive Value RNAalifold(seed): 0.871 RSpredict(seed): 0.703 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.661 Carnac(seed): 0.425 Sensitivity RNAalifold(seed): 0.501 Carnac(seed): 0.201 Positive Predictive Value RNAalifold(seed): 0.872 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.596 Mastr(seed): 0.297 Sensitivity RNAalifold(seed): 0.397 Mastr(seed): 0.099 Positive Predictive Value RNAalifold(seed): 0.897 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RNAalifold(seed): 0.706 Sensitivity PETfold_2.0(seed): 0.684 RNAalifold(seed): 0.500 Positive Predictive Value PETfold_2.0(seed): 0.897 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
HotKnots	39 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.673 HotKnots: 0.532 Sensitivity CentroidAlifold(20): 0.516 HotKnots: 0.477 Positive Predictive Value CentroidAlifold(20): 0.879 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 HotKnots: 0.504 Sensitivity PETfold_pre2.0(seed): 0.595 HotKnots: 0.450 Positive Predictive Value PETfold_pre2.0(seed): 0.879 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.633 HotKnots: 0.549 Sensitivity ContextFold: 0.523 HotKnots: 0.485 Positive Predictive Value ContextFold: 0.769 HotKnots: 0.626 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.666 HotKnots: 0.581 Sensitivity MXScarna(seed): 0.554 HotKnots: 0.528 Positive Predictive Value MXScarna(seed): 0.804 HotKnots: 0.643 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.656 HotKnots: 0.556 Sensitivity RNAalifold(20): 0.502 HotKnots: 0.495 Positive Predictive Value RNAalifold(20): 0.860 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 HotKnots: 0.474 Sensitivity PETfold_pre2.0(20): 0.530 HotKnots: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.798 HotKnots: 0.535 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08	15 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.691 HotKnots: 0.555 Sensitivity PPfold(20): 0.544 HotKnots: 0.490 Positive Predictive Value PPfold(20): 0.881 HotKnots: 0.636 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.05041766982e-08	55 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.615 HotKnots: 0.560 Sensitivity IPknot: 0.512 HotKnots: 0.493 Positive Predictive Value IPknot: 0.742 HotKnots: 0.639 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 HotKnots: 0.568 Sensitivity CentroidAlifold(seed): 0.397 HotKnots: 0.516 Positive Predictive Value CentroidAlifold(seed): 0.889 HotKnots: 0.630 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	34 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.623 HotKnots: 0.556 Sensitivity RNASampler(20): 0.470 HotKnots: 0.495 Positive Predictive Value RNASampler(20): 0.830 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.655 HotKnots: 0.555 Sensitivity TurboFold(20): 0.529 HotKnots: 0.490 Positive Predictive Value TurboFold(20): 0.816 HotKnots: 0.636 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	34 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.624 HotKnots: 0.556 Sensitivity MXScarna(20): 0.518 HotKnots: 0.495 Positive Predictive Value MXScarna(20): 0.756 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.640 HotKnots: 0.622 Sensitivity Sfold: 0.548 HotKnots: 0.558 Positive Predictive Value Sfold: 0.751 HotKnots: 0.699 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.600 CentroidHomfold‑LAST: 0.587 Sensitivity HotKnots: 0.525 CentroidHomfold‑LAST: 0.439 Positive Predictive Value HotKnots: 0.691 CentroidHomfold‑LAST: 0.789 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 2.28033735003e-07	135 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.622 Contrafold: 0.618 Sensitivity HotKnots: 0.558 Contrafold: 0.550 Positive Predictive Value HotKnots: 0.699 Contrafold: 0.700 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00985919189012	33 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.596 HotKnots: 0.579 Sensitivity RNAalifold(seed): 0.397 HotKnots: 0.532 Positive Predictive Value RNAalifold(seed): 0.897 HotKnots: 0.635 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.97386617324e-07		+ HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.617 MaxExpect: 0.610 Sensitivity HotKnots: 0.556 MaxExpect: 0.539 Positive Predictive Value HotKnots: 0.690 MaxExpect: 0.695 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 1.50402730567e-05	+ HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: 0.609 CentroidFold: 0.601 Sensitivity HotKnots: 0.548 CentroidFold: 0.515 Positive Predictive Value HotKnots: 0.681 CentroidFold: 0.706 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.98094999346e-07	- UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.624 HotKnots: 0.622 Sensitivity UNAFold: 0.554 HotKnots: 0.558 Positive Predictive Value UNAFold: 0.707 HotKnots: 0.699 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.000474528565072	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.622 PknotsRG: 0.608 Sensitivity HotKnots: 0.558 PknotsRG: 0.544 Positive Predictive Value HotKnots: 0.699 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.606 ProbKnot: 0.594 Sensitivity HotKnots: 0.546 ProbKnot: 0.537 Positive Predictive Value HotKnots: 0.676 ProbKnot: 0.661 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 9.49173053431e-08	- Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.577 HotKnots: 0.556 Sensitivity Murlet(20): 0.423 HotKnots: 0.495 Positive Predictive Value Murlet(20): 0.791 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.622 RNAfold: 0.613 Sensitivity HotKnots: 0.558 RNAfold: 0.547 Positive Predictive Value HotKnots: 0.699 RNAfold: 0.691 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.85233844192e-08	- Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.577 HotKnots: 0.556 Sensitivity Carnac(20): 0.372 HotKnots: 0.495 Positive Predictive Value Carnac(20): 0.897 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.622 RNAshapes: 0.602 Sensitivity HotKnots: 0.558 RNAshapes: 0.533 Positive Predictive Value HotKnots: 0.699 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.623 Fold: 0.605 Sensitivity HotKnots: 0.562 Fold: 0.544 Positive Predictive Value HotKnots: 0.694 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 8.81311508309e-08	= TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.544 HotKnots: 0.523 Sensitivity TurboFold(seed): 0.439 HotKnots: 0.464 Positive Predictive Value TurboFold(seed): 0.679 HotKnots: 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0017676675921	- RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.544 HotKnots: 0.535 Sensitivity RSpredict(20): 0.425 HotKnots: 0.482 Positive Predictive Value RSpredict(20): 0.701 HotKnots: 0.600 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000150377120024	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.639 Afold: 0.615 Sensitivity HotKnots: 0.583 Afold: 0.563 Positive Predictive Value HotKnots: 0.705 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.622 RNAsubopt: 0.595 Sensitivity HotKnots: 0.558 RNAsubopt: 0.534 Positive Predictive Value HotKnots: 0.699 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.549 RNASLOpt: 0.489 Sensitivity HotKnots: 0.485 RNASLOpt: 0.393 Positive Predictive Value HotKnots: 0.626 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.652 Cylofold: 0.607 Sensitivity HotKnots: 0.584 Cylofold: 0.517 Positive Predictive Value HotKnots: 0.734 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.621 McQFold: 0.571 Sensitivity HotKnots: 0.557 McQFold: 0.492 Positive Predictive Value HotKnots: 0.697 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.599 Multilign(20): 0.561 Sensitivity HotKnots: 0.524 Multilign(20): 0.466 Positive Predictive Value HotKnots: 0.690 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.626 CRWrnafold: 0.585 Sensitivity HotKnots: 0.569 CRWrnafold: 0.522 Positive Predictive Value HotKnots: 0.695 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.655 Pknots: 0.601 Sensitivity HotKnots: 0.588 Pknots: 0.545 Positive Predictive Value HotKnots: 0.735 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.635 HotKnots: 0.620 Sensitivity RNASampler(seed): 0.484 HotKnots: 0.579 Positive Predictive Value RNASampler(seed): 0.837 HotKnots: 0.669 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.31679015848e-06	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.719 Alterna: 0.665 Sensitivity HotKnots: 0.645 Alterna: 0.599 Positive Predictive Value HotKnots: 0.808 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.556 Mastr(20): 0.514 Sensitivity HotKnots: 0.495 Mastr(20): 0.339 Positive Predictive Value HotKnots: 0.628 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.642 Vsfold4: 0.547 Sensitivity HotKnots: 0.578 Vsfold4: 0.465 Positive Predictive Value HotKnots: 0.718 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.615 Murlet(seed): 0.514 Sensitivity HotKnots: 0.552 Murlet(seed): 0.315 Positive Predictive Value HotKnots: 0.689 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.639 Vsfold5: 0.510 Sensitivity HotKnots: 0.575 Vsfold5: 0.441 Positive Predictive Value HotKnots: 0.715 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.643 MCFold: 0.522 Sensitivity HotKnots: 0.583 MCFold: 0.535 Positive Predictive Value HotKnots: 0.715 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.715 RDfolder: 0.592 Sensitivity HotKnots: 0.644 RDfolder: 0.491 Positive Predictive Value HotKnots: 0.802 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.551 RNAwolf: 0.385 Sensitivity HotKnots: 0.489 RNAwolf: 0.360 Positive Predictive Value HotKnots: 0.627 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: 0.579 CMfinder(20): 0.546 Sensitivity HotKnots: 0.500 CMfinder(20): 0.366 Positive Predictive Value HotKnots: 0.678 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.582 NanoFolder: 0.339 Sensitivity HotKnots: 0.518 NanoFolder: 0.350 Positive Predictive Value HotKnots: 0.660 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.558 HotKnots: 0.501 Sensitivity Multilign(seed): 0.434 HotKnots: 0.437 Positive Predictive Value Multilign(seed): 0.725 HotKnots: 0.581 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.524 PPfold(seed): 0.092 Sensitivity HotKnots: 0.458 PPfold(seed): 0.016 Positive Predictive Value HotKnots: 0.605 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.571 RSpredict(seed): 0.266 Sensitivity HotKnots: 0.521 RSpredict(seed): 0.128 Positive Predictive Value HotKnots: 0.632 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.626 Carnac(seed): 0.241 Sensitivity HotKnots: 0.565 Carnac(seed): 0.058 Positive Predictive Value HotKnots: 0.698 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.578 Mastr(seed): 0.236 Sensitivity HotKnots: 0.524 Mastr(seed): 0.062 Positive Predictive Value HotKnots: 0.643 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 HotKnots: 0.682 Sensitivity PETfold_2.0(seed): 0.642 HotKnots: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 HotKnots: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 HotKnots: 0.541 Sensitivity PETfold_2.0(20): 0.509 HotKnots: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MaxExpect	39 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.673 MaxExpect: 0.553 Sensitivity CentroidAlifold(20): 0.516 MaxExpect: 0.480 Positive Predictive Value CentroidAlifold(20): 0.879 MaxExpect: 0.641 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 MaxExpect: 0.509 Sensitivity PETfold_pre2.0(seed): 0.602 MaxExpect: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.850 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	49 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.563 MaxExpect: 0.473 Sensitivity ContextFold: 0.466 MaxExpect: 0.409 Positive Predictive Value ContextFold: 0.681 MaxExpect: 0.549 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.663 MaxExpect: 0.572 Sensitivity MXScarna(seed): 0.557 MaxExpect: 0.506 Positive Predictive Value MXScarna(seed): 0.789 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.655 MaxExpect: 0.580 Sensitivity RNAalifold(20): 0.504 MaxExpect: 0.503 Positive Predictive Value RNAalifold(20): 0.855 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MaxExpect: 0.481 Sensitivity PETfold_pre2.0(20): 0.530 MaxExpect: 0.412 Positive Predictive Value PETfold_pre2.0(20): 0.798 MaxExpect: 0.568 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	15 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.691 MaxExpect: 0.563 Sensitivity PPfold(20): 0.544 MaxExpect: 0.474 Positive Predictive Value PPfold(20): 0.881 MaxExpect: 0.673 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.30280588002e-08	57 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.554 MaxExpect: 0.483 Sensitivity IPknot: 0.448 MaxExpect: 0.418 Positive Predictive Value IPknot: 0.688 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.626 MaxExpect: 0.565 Sensitivity CentroidAlifold(seed): 0.446 MaxExpect: 0.498 Positive Predictive Value CentroidAlifold(seed): 0.879 MaxExpect: 0.641 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.625 MaxExpect: 0.580 Sensitivity RNASampler(20): 0.475 MaxExpect: 0.503 Positive Predictive Value RNASampler(20): 0.826 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.655 MaxExpect: 0.563 Sensitivity TurboFold(20): 0.529 MaxExpect: 0.474 Positive Predictive Value TurboFold(20): 0.816 MaxExpect: 0.673 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	32 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.626 MaxExpect: 0.580 Sensitivity MXScarna(20): 0.520 MaxExpect: 0.503 Positive Predictive Value MXScarna(20): 0.756 MaxExpect: 0.674 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.552 Sfold: 0.544 Sensitivity MaxExpect: 0.480 Sfold: 0.460 Positive Predictive Value MaxExpect: 0.635 Sfold: 0.645 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.000150377120024	56 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 MaxExpect: 0.563 Sensitivity CentroidHomfold‑LAST: 0.439 MaxExpect: 0.486 Positive Predictive Value CentroidHomfold‑LAST: 0.789 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.561 MaxExpect: 0.552 Sensitivity Contrafold: 0.489 MaxExpect: 0.480 Positive Predictive Value Contrafold: 0.644 MaxExpect: 0.635 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 6.53888633552e-08	32 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.630 MaxExpect: 0.548 Sensitivity RNAalifold(seed): 0.460 MaxExpect: 0.485 Positive Predictive Value RNAalifold(seed): 0.863 MaxExpect: 0.621 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	115 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.617 MaxExpect: 0.610 Sensitivity HotKnots: 0.556 MaxExpect: 0.539 Positive Predictive Value HotKnots: 0.690 MaxExpect: 0.695 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 1.50402730567e-05		- CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.554 MaxExpect: 0.549 Sensitivity CentroidFold: 0.455 MaxExpect: 0.477 Positive Predictive Value CentroidFold: 0.674 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.09925167801e-06	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.552 UNAFold: 0.527 Sensitivity MaxExpect: 0.480 UNAFold: 0.463 Positive Predictive Value MaxExpect: 0.635 UNAFold: 0.600 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 1.02208072244e-07	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.559 PknotsRG: 0.517 Sensitivity MaxExpect: 0.486 PknotsRG: 0.459 Positive Predictive Value MaxExpect: 0.645 PknotsRG: 0.583 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.541 ProbKnot: 0.536 Sensitivity MaxExpect: 0.476 ProbKnot: 0.480 Positive Predictive Value MaxExpect: 0.616 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.580 Murlet(20): 0.576 Sensitivity MaxExpect: 0.503 Murlet(20): 0.424 Positive Predictive Value MaxExpect: 0.674 Murlet(20): 0.786 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.000609097173132	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.552 RNAfold: 0.519 Sensitivity MaxExpect: 0.480 RNAfold: 0.459 Positive Predictive Value MaxExpect: 0.635 RNAfold: 0.587 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.580 Carnac(20): 0.578 Sensitivity MaxExpect: 0.503 Carnac(20): 0.375 Positive Predictive Value MaxExpect: 0.674 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.518809073978	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.610 RNAshapes: 0.600 Sensitivity MaxExpect: 0.539 RNAshapes: 0.533 Positive Predictive Value MaxExpect: 0.695 RNAshapes: 0.679 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.553 Fold: 0.535 Sensitivity MaxExpect: 0.487 Fold: 0.481 Positive Predictive Value MaxExpect: 0.628 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.544 MaxExpect: 0.506 Sensitivity TurboFold(seed): 0.439 MaxExpect: 0.418 Positive Predictive Value TurboFold(seed): 0.679 MaxExpect: 0.620 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.555 RSpredict(20): 0.541 Sensitivity MaxExpect: 0.483 RSpredict(20): 0.422 Positive Predictive Value MaxExpect: 0.641 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.555 Afold: 0.511 Sensitivity MaxExpect: 0.487 Afold: 0.458 Positive Predictive Value MaxExpect: 0.633 Afold: 0.571 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.610 RNAsubopt: 0.595 Sensitivity MaxExpect: 0.539 RNAsubopt: 0.536 Positive Predictive Value MaxExpect: 0.695 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.531 RNASLOpt: 0.489 Sensitivity MaxExpect: 0.454 RNASLOpt: 0.393 Positive Predictive Value MaxExpect: 0.626 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.651 Cylofold: 0.607 Sensitivity MaxExpect: 0.574 Cylofold: 0.517 Positive Predictive Value MaxExpect: 0.744 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.551 McQFold: 0.454 Sensitivity MaxExpect: 0.479 McQFold: 0.388 Positive Predictive Value MaxExpect: 0.634 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.561 MaxExpect: 0.547 Sensitivity Multilign(20): 0.466 MaxExpect: 0.476 Positive Predictive Value Multilign(20): 0.682 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	- CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.585 MaxExpect: 0.576 Sensitivity CRWrnafold: 0.522 MaxExpect: 0.511 Positive Predictive Value CRWrnafold: 0.663 MaxExpect: 0.656 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.47427610203e-05	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.659 Pknots: 0.598 Sensitivity MaxExpect: 0.584 Pknots: 0.544 Positive Predictive Value MaxExpect: 0.750 Pknots: 0.664 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.644 RNASampler(seed): 0.623 Sensitivity MaxExpect: 0.578 RNASampler(seed): 0.475 Positive Predictive Value MaxExpect: 0.722 RNASampler(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.54671126599e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.713 Alterna: 0.654 Sensitivity MaxExpect: 0.636 Alterna: 0.593 Positive Predictive Value MaxExpect: 0.805 Alterna: 0.729 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.580 Mastr(20): 0.511 Sensitivity MaxExpect: 0.503 Mastr(20): 0.335 Positive Predictive Value MaxExpect: 0.674 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.638 Vsfold4: 0.543 Sensitivity MaxExpect: 0.568 Vsfold4: 0.462 Positive Predictive Value MaxExpect: 0.720 Vsfold4: 0.643 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.613 Murlet(seed): 0.512 Sensitivity MaxExpect: 0.533 Murlet(seed): 0.315 Positive Predictive Value MaxExpect: 0.711 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.630 Vsfold5: 0.500 Sensitivity MaxExpect: 0.561 Vsfold5: 0.432 Positive Predictive Value MaxExpect: 0.712 Vsfold5: 0.584 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.629 MCFold: 0.501 Sensitivity MaxExpect: 0.559 MCFold: 0.517 Positive Predictive Value MaxExpect: 0.713 MCFold: 0.495 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.702 RDfolder: 0.586 Sensitivity MaxExpect: 0.625 RDfolder: 0.486 Positive Predictive Value MaxExpect: 0.795 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.485 RNAwolf: 0.356 Sensitivity MaxExpect: 0.421 RNAwolf: 0.331 Positive Predictive Value MaxExpect: 0.561 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.553 CMfinder(20): 0.546 Sensitivity MaxExpect: 0.470 CMfinder(20): 0.366 Positive Predictive Value MaxExpect: 0.658 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.587 NanoFolder: 0.339 Sensitivity MaxExpect: 0.512 NanoFolder: 0.350 Positive Predictive Value MaxExpect: 0.677 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	? MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.580 Multilign(seed): 0.558 Sensitivity MaxExpect: 0.469 Multilign(seed): 0.434 Positive Predictive Value MaxExpect: 0.724 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.544 PPfold(seed): 0.092 Sensitivity MaxExpect: 0.455 PPfold(seed): 0.016 Positive Predictive Value MaxExpect: 0.657 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.566 RSpredict(seed): 0.374 Sensitivity MaxExpect: 0.500 RSpredict(seed): 0.220 Positive Predictive Value MaxExpect: 0.642 RSpredict(seed): 0.637 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.579 Carnac(seed): 0.402 Sensitivity MaxExpect: 0.507 Carnac(seed): 0.180 Positive Predictive Value MaxExpect: 0.661 Carnac(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.600 Mastr(seed): 0.247 Sensitivity MaxExpect: 0.532 Mastr(seed): 0.068 Positive Predictive Value MaxExpect: 0.682 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MaxExpect: 0.657 Sensitivity PETfold_2.0(seed): 0.642 MaxExpect: 0.558 Positive Predictive Value PETfold_2.0(seed): 0.924 MaxExpect: 0.779 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MaxExpect: 0.498 Sensitivity PETfold_2.0(20): 0.509 MaxExpect: 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidFold	39 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 CentroidFold: 0.537 Sensitivity CentroidAlifold(20): 0.516 CentroidFold: 0.456 Positive Predictive Value CentroidAlifold(20): 0.879 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidFold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	61 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.566 CentroidFold: 0.476 Sensitivity ContextFold: 0.469 CentroidFold: 0.385 Positive Predictive Value ContextFold: 0.684 CentroidFold: 0.591 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.657 CentroidFold: 0.578 Sensitivity MXScarna(seed): 0.550 CentroidFold: 0.496 Positive Predictive Value MXScarna(seed): 0.787 CentroidFold: 0.674 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.646 CentroidFold: 0.537 Sensitivity RNAalifold(20): 0.499 CentroidFold: 0.456 Positive Predictive Value RNAalifold(20): 0.838 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidFold: 0.445 Sensitivity PETfold_pre2.0(20): 0.530 CentroidFold: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	21 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.662 CentroidFold: 0.487 Sensitivity PPfold(20): 0.526 CentroidFold: 0.413 Positive Predictive Value PPfold(20): 0.837 CentroidFold: 0.581 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	69 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.549 CentroidFold: 0.489 Sensitivity IPknot: 0.446 CentroidFold: 0.396 Positive Predictive Value IPknot: 0.678 CentroidFold: 0.606 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 CentroidFold: 0.577 Sensitivity CentroidAlifold(seed): 0.443 CentroidFold: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.880 CentroidFold: 0.672 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.609 CentroidFold: 0.537 Sensitivity RNASampler(20): 0.466 CentroidFold: 0.456 Positive Predictive Value RNASampler(20): 0.800 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.625 CentroidFold: 0.487 Sensitivity TurboFold(20): 0.518 CentroidFold: 0.413 Positive Predictive Value TurboFold(20): 0.759 CentroidFold: 0.581 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	39 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.617 CentroidFold: 0.537 Sensitivity MXScarna(20): 0.514 CentroidFold: 0.456 Positive Predictive Value MXScarna(20): 0.743 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.529 Sfold: 0.520 Sensitivity CentroidFold: 0.442 Sfold: 0.443 Positive Predictive Value CentroidFold: 0.634 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 6.53888633552e-08	67 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.578 CentroidFold: 0.548 Sensitivity CentroidHomfold‑LAST: 0.440 CentroidFold: 0.458 Positive Predictive Value CentroidHomfold‑LAST: 0.763 CentroidFold: 0.661 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 Contrafold vs CentroidFold Matthews Correlation Coefficient Contrafold: 0.532 CentroidFold: 0.529 Sensitivity Contrafold: 0.472 CentroidFold: 0.442 Positive Predictive Value Contrafold: 0.601 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 9.94962292175e-07	37 RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.625 CentroidFold: 0.585 Sensitivity RNAalifold(seed): 0.449 CentroidFold: 0.499 Positive Predictive Value RNAalifold(seed): 0.871 CentroidFold: 0.686 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	133 HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: 0.609 CentroidFold: 0.601 Sensitivity HotKnots: 0.548 CentroidFold: 0.515 Positive Predictive Value HotKnots: 0.681 CentroidFold: 0.706 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.98094999346e-07	130 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.554 MaxExpect: 0.549 Sensitivity CentroidFold: 0.455 MaxExpect: 0.477 Positive Predictive Value CentroidFold: 0.674 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.09925167801e-06		+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.529 UNAFold: 0.498 Sensitivity CentroidFold: 0.442 UNAFold: 0.446 Positive Predictive Value CentroidFold: 0.634 UNAFold: 0.556 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.525 PknotsRG: 0.492 Sensitivity CentroidFold: 0.438 PknotsRG: 0.446 Positive Predictive Value CentroidFold: 0.631 PknotsRG: 0.543 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.541 ProbKnot: 0.532 Sensitivity CentroidFold: 0.450 ProbKnot: 0.475 Positive Predictive Value CentroidFold: 0.652 ProbKnot: 0.597 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 4.32815307575e-07	- Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.582 CentroidFold: 0.537 Sensitivity Murlet(20): 0.430 CentroidFold: 0.456 Positive Predictive Value Murlet(20): 0.793 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.529 RNAfold: 0.492 Sensitivity CentroidFold: 0.442 RNAfold: 0.445 Positive Predictive Value CentroidFold: 0.634 RNAfold: 0.546 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.579 CentroidFold: 0.537 Sensitivity Carnac(20): 0.374 CentroidFold: 0.456 Positive Predictive Value Carnac(20): 0.899 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.601 RNAshapes: 0.586 Sensitivity CentroidFold: 0.515 RNAshapes: 0.521 Positive Predictive Value CentroidFold: 0.706 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.556 Fold: 0.531 Sensitivity CentroidFold: 0.464 Fold: 0.476 Positive Predictive Value CentroidFold: 0.668 Fold: 0.593 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.547 CentroidFold: 0.514 Sensitivity TurboFold(seed): 0.452 CentroidFold: 0.413 Positive Predictive Value TurboFold(seed): 0.667 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	= RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.541 CentroidFold: 0.540 Sensitivity RSpredict(20): 0.422 CentroidFold: 0.459 Positive Predictive Value RSpredict(20): 0.699 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.777738600652	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.524 Afold: 0.469 Sensitivity CentroidFold: 0.439 Afold: 0.431 Positive Predictive Value CentroidFold: 0.625 Afold: 0.510 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.601 RNAsubopt: 0.590 Sensitivity CentroidFold: 0.515 RNAsubopt: 0.531 Positive Predictive Value CentroidFold: 0.706 RNAsubopt: 0.659 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.508 RNASLOpt: 0.488 Sensitivity CentroidFold: 0.422 RNASLOpt: 0.395 Positive Predictive Value CentroidFold: 0.617 RNASLOpt: 0.607 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.653 Cylofold: 0.603 Sensitivity CentroidFold: 0.564 Cylofold: 0.515 Positive Predictive Value CentroidFold: 0.763 Cylofold: 0.713 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.528 McQFold: 0.432 Sensitivity CentroidFold: 0.441 McQFold: 0.345 Positive Predictive Value CentroidFold: 0.633 McQFold: 0.541 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.526 CentroidFold: 0.472 Sensitivity Multilign(20): 0.437 CentroidFold: 0.406 Positive Predictive Value Multilign(20): 0.640 CentroidFold: 0.556 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.639 CRWrnafold: 0.585 Sensitivity CentroidFold: 0.545 CRWrnafold: 0.522 Positive Predictive Value CentroidFold: 0.757 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.633 Pknots: 0.586 Sensitivity CentroidFold: 0.547 Pknots: 0.532 Positive Predictive Value CentroidFold: 0.739 Pknots: 0.652 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.647 RNASampler(seed): 0.586 Sensitivity CentroidFold: 0.556 RNASampler(seed): 0.440 Positive Predictive Value CentroidFold: 0.758 RNASampler(seed): 0.787 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.738 Alterna: 0.651 Sensitivity CentroidFold: 0.643 Alterna: 0.590 Positive Predictive Value CentroidFold: 0.853 Alterna: 0.728 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.537 Mastr(20): 0.499 Sensitivity CentroidFold: 0.456 Mastr(20): 0.333 Positive Predictive Value CentroidFold: 0.637 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.625 Vsfold4: 0.524 Sensitivity CentroidFold: 0.543 Vsfold4: 0.445 Positive Predictive Value CentroidFold: 0.723 Vsfold4: 0.624 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.619 Murlet(seed): 0.503 Sensitivity CentroidFold: 0.521 Murlet(seed): 0.299 Positive Predictive Value CentroidFold: 0.739 Murlet(seed): 0.851 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.626 Vsfold5: 0.491 Sensitivity CentroidFold: 0.544 Vsfold5: 0.425 Positive Predictive Value CentroidFold: 0.726 Vsfold5: 0.574 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.630 MCFold: 0.510 Sensitivity CentroidFold: 0.546 MCFold: 0.525 Positive Predictive Value CentroidFold: 0.734 MCFold: 0.503 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.729 RDfolder: 0.579 Sensitivity CentroidFold: 0.635 RDfolder: 0.480 Positive Predictive Value CentroidFold: 0.844 RDfolder: 0.709 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.489 RNAwolf: 0.356 Sensitivity CentroidFold: 0.396 RNAwolf: 0.331 Positive Predictive Value CentroidFold: 0.606 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidFold: 0.393 Sensitivity CMfinder(20): 0.366 CentroidFold: 0.344 Positive Predictive Value CMfinder(20): 0.748 CentroidFold: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.524 NanoFolder: 0.337 Sensitivity CentroidFold: 0.447 NanoFolder: 0.350 Positive Predictive Value CentroidFold: 0.621 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.578 CentroidFold: 0.570 Sensitivity Multilign(seed): 0.454 CentroidFold: 0.443 Positive Predictive Value Multilign(seed): 0.743 CentroidFold: 0.738 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.41366350922e-05	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.511 PPfold(seed): 0.148 Sensitivity CentroidFold: 0.426 PPfold(seed): 0.032 Positive Predictive Value CentroidFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.579 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.498 RSpredict(seed): 0.218 Positive Predictive Value CentroidFold: 0.674 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.603 Carnac(seed): 0.396 Sensitivity CentroidFold: 0.512 Carnac(seed): 0.173 Positive Predictive Value CentroidFold: 0.712 Carnac(seed): 0.905 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.579 Mastr(seed): 0.219 Sensitivity CentroidFold: 0.501 Mastr(seed): 0.055 Positive Predictive Value CentroidFold: 0.674 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidFold: 0.506 Sensitivity PETfold_2.0(seed): 0.642 CentroidFold: 0.421 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidFold: 0.615 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidFold: 0.467 Sensitivity PETfold_2.0(20): 0.509 CentroidFold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
UNAFold	39 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 UNAFold: 0.541 Sensitivity CentroidAlifold(20): 0.516 UNAFold: 0.477 Positive Predictive Value CentroidAlifold(20): 0.879 UNAFold: 0.619 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.602 UNAFold: 0.414 Positive Predictive Value PETfold_pre2.0(seed): 0.850 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.563 UNAFold: 0.469 Sensitivity ContextFold: 0.466 UNAFold: 0.412 Positive Predictive Value ContextFold: 0.681 UNAFold: 0.534 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.667 UNAFold: 0.555 Sensitivity MXScarna(seed): 0.560 UNAFold: 0.495 Positive Predictive Value MXScarna(seed): 0.794 UNAFold: 0.625 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.656 UNAFold: 0.572 Sensitivity RNAalifold(20): 0.502 UNAFold: 0.501 Positive Predictive Value RNAalifold(20): 0.860 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 UNAFold: 0.462 Sensitivity PETfold_pre2.0(20): 0.530 UNAFold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 UNAFold: 0.531 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	15 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.691 UNAFold: 0.555 Sensitivity PPfold(20): 0.544 UNAFold: 0.482 Positive Predictive Value PPfold(20): 0.881 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	57 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.554 UNAFold: 0.480 Sensitivity IPknot: 0.448 UNAFold: 0.421 Positive Predictive Value IPknot: 0.688 UNAFold: 0.547 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 UNAFold: 0.546 Sensitivity CentroidAlifold(seed): 0.443 UNAFold: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.880 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.623 UNAFold: 0.572 Sensitivity RNASampler(20): 0.470 UNAFold: 0.501 Positive Predictive Value RNASampler(20): 0.830 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.655 UNAFold: 0.555 Sensitivity TurboFold(20): 0.529 UNAFold: 0.482 Positive Predictive Value TurboFold(20): 0.816 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	34 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.624 UNAFold: 0.572 Sensitivity MXScarna(20): 0.518 UNAFold: 0.501 Positive Predictive Value MXScarna(20): 0.756 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.508 UNAFold: 0.489 Sensitivity Sfold: 0.432 UNAFold: 0.434 Positive Predictive Value Sfold: 0.599 UNAFold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 UNAFold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.439 UNAFold: 0.501 Positive Predictive Value CentroidHomfold‑LAST: 0.789 UNAFold: 0.665 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 2.38297003775e-06	140 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.542 UNAFold: 0.489 Sensitivity Contrafold: 0.477 UNAFold: 0.434 Positive Predictive Value Contrafold: 0.616 UNAFold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 UNAFold: 0.541 Sensitivity RNAalifold(seed): 0.460 UNAFold: 0.483 Positive Predictive Value RNAalifold(seed): 0.866 UNAFold: 0.608 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.624 HotKnots: 0.622 Sensitivity UNAFold: 0.554 HotKnots: 0.558 Positive Predictive Value UNAFold: 0.707 HotKnots: 0.699 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.000474528565072	118 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.552 UNAFold: 0.527 Sensitivity MaxExpect: 0.480 UNAFold: 0.463 Positive Predictive Value MaxExpect: 0.635 UNAFold: 0.600 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 1.02208072244e-07	137 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.529 UNAFold: 0.498 Sensitivity CentroidFold: 0.442 UNAFold: 0.446 Positive Predictive Value CentroidFold: 0.634 UNAFold: 0.556 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.490 PknotsRG: 0.478 Sensitivity UNAFold: 0.436 PknotsRG: 0.430 Positive Predictive Value UNAFold: 0.551 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	= UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.537 ProbKnot: 0.536 Sensitivity UNAFold: 0.478 ProbKnot: 0.480 Positive Predictive Value UNAFold: 0.605 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.206416030449	= Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.577 UNAFold: 0.572 Sensitivity Murlet(20): 0.423 UNAFold: 0.501 Positive Predictive Value Murlet(20): 0.791 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0223116232526	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.489 RNAfold: 0.484 Sensitivity UNAFold: 0.434 RNAfold: 0.434 Positive Predictive Value UNAFold: 0.550 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.577 UNAFold: 0.572 Sensitivity Carnac(20): 0.372 UNAFold: 0.501 Positive Predictive Value Carnac(20): 0.897 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.000218715568349	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.624 RNAshapes: 0.602 Sensitivity UNAFold: 0.554 RNAshapes: 0.533 Positive Predictive Value UNAFold: 0.707 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.553 Fold: 0.535 Sensitivity UNAFold: 0.492 Fold: 0.481 Positive Predictive Value UNAFold: 0.622 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 4.48494289621e-08	- TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.544 UNAFold: 0.484 Sensitivity TurboFold(seed): 0.439 UNAFold: 0.418 Positive Predictive Value TurboFold(seed): 0.679 UNAFold: 0.568 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	= UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.545 RSpredict(20): 0.544 Sensitivity UNAFold: 0.482 RSpredict(20): 0.425 Positive Predictive Value UNAFold: 0.620 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.736846409308	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.474 Afold: 0.468 Sensitivity UNAFold: 0.425 Afold: 0.425 Positive Predictive Value UNAFold: 0.529 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.624 RNAsubopt: 0.595 Sensitivity UNAFold: 0.554 RNAsubopt: 0.534 Positive Predictive Value UNAFold: 0.707 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.532 RNASLOpt: 0.489 Sensitivity UNAFold: 0.466 RNASLOpt: 0.393 Positive Predictive Value UNAFold: 0.611 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.637 Cylofold: 0.607 Sensitivity UNAFold: 0.566 Cylofold: 0.517 Positive Predictive Value UNAFold: 0.724 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.488 McQFold: 0.415 Sensitivity UNAFold: 0.434 McQFold: 0.332 Positive Predictive Value UNAFold: 0.549 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.569 Multilign(20): 0.561 Sensitivity UNAFold: 0.495 Multilign(20): 0.466 Positive Predictive Value UNAFold: 0.661 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.83111007457e-05	= UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.590 CRWrnafold: 0.585 Sensitivity UNAFold: 0.530 CRWrnafold: 0.522 Positive Predictive Value UNAFold: 0.664 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.288298117014	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.661 Pknots: 0.601 Sensitivity UNAFold: 0.587 Pknots: 0.545 Positive Predictive Value UNAFold: 0.750 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.639 RNASampler(seed): 0.635 Sensitivity UNAFold: 0.584 RNASampler(seed): 0.484 Positive Predictive Value UNAFold: 0.704 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7981009876e-07	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.722 Alterna: 0.665 Sensitivity UNAFold: 0.642 Alterna: 0.599 Positive Predictive Value UNAFold: 0.819 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.572 Mastr(20): 0.514 Sensitivity UNAFold: 0.501 Mastr(20): 0.339 Positive Predictive Value UNAFold: 0.658 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.643 Vsfold4: 0.547 Sensitivity UNAFold: 0.573 Vsfold4: 0.465 Positive Predictive Value UNAFold: 0.726 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.615 Murlet(seed): 0.514 Sensitivity UNAFold: 0.543 Murlet(seed): 0.315 Positive Predictive Value UNAFold: 0.702 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.637 Vsfold5: 0.510 Sensitivity UNAFold: 0.568 Vsfold5: 0.441 Positive Predictive Value UNAFold: 0.719 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.647 MCFold: 0.522 Sensitivity UNAFold: 0.579 MCFold: 0.535 Positive Predictive Value UNAFold: 0.730 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.709 RDfolder: 0.592 Sensitivity UNAFold: 0.631 RDfolder: 0.491 Positive Predictive Value UNAFold: 0.805 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.483 RNAwolf: 0.356 Sensitivity UNAFold: 0.424 RNAwolf: 0.331 Positive Predictive Value UNAFold: 0.551 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.570 CMfinder(20): 0.546 Sensitivity UNAFold: 0.494 CMfinder(20): 0.366 Positive Predictive Value UNAFold: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.556 NanoFolder: 0.339 Sensitivity UNAFold: 0.489 NanoFolder: 0.350 Positive Predictive Value UNAFold: 0.639 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.558 UNAFold: 0.501 Sensitivity Multilign(seed): 0.434 UNAFold: 0.427 Positive Predictive Value Multilign(seed): 0.725 UNAFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.500 PPfold(seed): 0.092 Sensitivity UNAFold: 0.432 PPfold(seed): 0.016 Positive Predictive Value UNAFold: 0.587 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.548 RSpredict(seed): 0.375 Sensitivity UNAFold: 0.488 RSpredict(seed): 0.220 Positive Predictive Value UNAFold: 0.616 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.570 Carnac(seed): 0.404 Sensitivity UNAFold: 0.504 Carnac(seed): 0.181 Positive Predictive Value UNAFold: 0.647 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.582 Mastr(seed): 0.236 Sensitivity UNAFold: 0.520 Mastr(seed): 0.062 Positive Predictive Value UNAFold: 0.655 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 UNAFold: 0.687 Sensitivity PETfold_2.0(seed): 0.642 UNAFold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 UNAFold: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 UNAFold: 0.549 Sensitivity PETfold_2.0(20): 0.509 UNAFold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 UNAFold: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PknotsRG	39 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.673 PknotsRG: 0.554 Sensitivity CentroidAlifold(20): 0.516 PknotsRG: 0.495 Positive Predictive Value CentroidAlifold(20): 0.879 PknotsRG: 0.626 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(seed): 0.595 PknotsRG: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.879 PknotsRG: 0.636 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	48 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.509 PknotsRG: 0.474 Sensitivity ContextFold: 0.419 PknotsRG: 0.419 Positive Predictive Value ContextFold: 0.620 PknotsRG: 0.538 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.666 PknotsRG: 0.592 Sensitivity MXScarna(seed): 0.554 PknotsRG: 0.537 Positive Predictive Value MXScarna(seed): 0.804 PknotsRG: 0.658 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.656 PknotsRG: 0.572 Sensitivity RNAalifold(20): 0.502 PknotsRG: 0.508 Positive Predictive Value RNAalifold(20): 0.860 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PknotsRG: 0.522 Sensitivity PETfold_pre2.0(20): 0.530 PknotsRG: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.798 PknotsRG: 0.593 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.691 PknotsRG: 0.588 Sensitivity PPfold(20): 0.544 PknotsRG: 0.516 Positive Predictive Value PPfold(20): 0.881 PknotsRG: 0.676 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	56 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.537 PknotsRG: 0.487 Sensitivity IPknot: 0.426 PknotsRG: 0.430 Positive Predictive Value IPknot: 0.678 PknotsRG: 0.553 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 PknotsRG: 0.585 Sensitivity CentroidAlifold(seed): 0.397 PknotsRG: 0.528 Positive Predictive Value CentroidAlifold(seed): 0.889 PknotsRG: 0.652 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 2.38297003775e-06	34 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.623 PknotsRG: 0.572 Sensitivity RNASampler(20): 0.470 PknotsRG: 0.508 Positive Predictive Value RNASampler(20): 0.830 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.655 PknotsRG: 0.588 Sensitivity TurboFold(20): 0.529 PknotsRG: 0.516 Positive Predictive Value TurboFold(20): 0.816 PknotsRG: 0.676 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	34 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.624 PknotsRG: 0.572 Sensitivity MXScarna(20): 0.518 PknotsRG: 0.508 Positive Predictive Value MXScarna(20): 0.756 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	139 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.511 PknotsRG: 0.478 Sensitivity Sfold: 0.433 PknotsRG: 0.430 Positive Predictive Value Sfold: 0.604 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 PknotsRG: 0.582 Sensitivity CentroidHomfold‑LAST: 0.439 PknotsRG: 0.509 Positive Predictive Value CentroidHomfold‑LAST: 0.789 PknotsRG: 0.670 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.0955699217783	139 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.539 PknotsRG: 0.478 Sensitivity Contrafold: 0.475 PknotsRG: 0.430 Positive Predictive Value Contrafold: 0.613 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.85233844192e-08	33 RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.596 PknotsRG: 0.593 Sensitivity RNAalifold(seed): 0.397 PknotsRG: 0.542 Positive Predictive Value RNAalifold(seed): 0.897 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.178906439528	135 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.622 PknotsRG: 0.608 Sensitivity HotKnots: 0.558 PknotsRG: 0.544 Positive Predictive Value HotKnots: 0.699 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.559 PknotsRG: 0.517 Sensitivity MaxExpect: 0.486 PknotsRG: 0.459 Positive Predictive Value MaxExpect: 0.645 PknotsRG: 0.583 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	136 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.525 PknotsRG: 0.492 Sensitivity CentroidFold: 0.438 PknotsRG: 0.446 Positive Predictive Value CentroidFold: 0.631 PknotsRG: 0.543 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.490 PknotsRG: 0.478 Sensitivity UNAFold: 0.436 PknotsRG: 0.430 Positive Predictive Value UNAFold: 0.551 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.548 ProbKnot: 0.544 Sensitivity PknotsRG: 0.493 ProbKnot: 0.490 Positive Predictive Value PknotsRG: 0.611 ProbKnot: 0.606 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 9.69999390915e-05	= Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.577 PknotsRG: 0.572 Sensitivity Murlet(20): 0.423 PknotsRG: 0.508 Positive Predictive Value Murlet(20): 0.791 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.00353686086758	- RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.486 PknotsRG: 0.478 Sensitivity RNAfold: 0.436 PknotsRG: 0.430 Positive Predictive Value RNAfold: 0.542 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.577 PknotsRG: 0.572 Sensitivity Carnac(20): 0.372 PknotsRG: 0.508 Positive Predictive Value Carnac(20): 0.897 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.00353686086758	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.608 RNAshapes: 0.602 Sensitivity PknotsRG: 0.544 RNAshapes: 0.533 Positive Predictive Value PknotsRG: 0.683 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.558 Fold: 0.550 Sensitivity PknotsRG: 0.503 Fold: 0.495 Positive Predictive Value PknotsRG: 0.621 Fold: 0.613 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 5.5212650266e-05	+ PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.559 TurboFold(seed): 0.544 Sensitivity PknotsRG: 0.491 TurboFold(seed): 0.439 Positive Predictive Value PknotsRG: 0.643 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.151222316e-07	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.558 RSpredict(20): 0.544 Sensitivity PknotsRG: 0.500 RSpredict(20): 0.425 Positive Predictive Value PknotsRG: 0.627 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 4.59499054376e-07	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.468 PknotsRG: 0.460 Sensitivity Afold: 0.425 PknotsRG: 0.417 Positive Predictive Value Afold: 0.517 PknotsRG: 0.507 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.608 RNAsubopt: 0.595 Sensitivity PknotsRG: 0.544 RNAsubopt: 0.534 Positive Predictive Value PknotsRG: 0.683 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.543 RNASLOpt: 0.489 Sensitivity PknotsRG: 0.477 RNASLOpt: 0.393 Positive Predictive Value PknotsRG: 0.622 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.639 Cylofold: 0.607 Sensitivity PknotsRG: 0.572 Cylofold: 0.517 Positive Predictive Value PknotsRG: 0.721 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.477 McQFold: 0.410 Sensitivity PknotsRG: 0.429 McQFold: 0.327 Positive Predictive Value PknotsRG: 0.531 McQFold: 0.516 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.602 Multilign(20): 0.561 Sensitivity PknotsRG: 0.530 Multilign(20): 0.466 Positive Predictive Value PknotsRG: 0.691 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.621 CRWrnafold: 0.585 Sensitivity PknotsRG: 0.563 CRWrnafold: 0.522 Positive Predictive Value PknotsRG: 0.692 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.645 Pknots: 0.601 Sensitivity PknotsRG: 0.578 Pknots: 0.545 Positive Predictive Value PknotsRG: 0.726 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.639 RNASampler(seed): 0.635 Sensitivity PknotsRG: 0.588 RNASampler(seed): 0.484 Positive Predictive Value PknotsRG: 0.699 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000481443120598	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.699 Alterna: 0.665 Sensitivity PknotsRG: 0.625 Alterna: 0.599 Positive Predictive Value PknotsRG: 0.789 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.572 Mastr(20): 0.514 Sensitivity PknotsRG: 0.508 Mastr(20): 0.339 Positive Predictive Value PknotsRG: 0.647 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.628 Vsfold4: 0.547 Sensitivity PknotsRG: 0.565 Vsfold4: 0.465 Positive Predictive Value PknotsRG: 0.703 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.634 Murlet(seed): 0.514 Sensitivity PknotsRG: 0.566 Murlet(seed): 0.315 Positive Predictive Value PknotsRG: 0.715 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.627 Vsfold5: 0.510 Sensitivity PknotsRG: 0.564 Vsfold5: 0.441 Positive Predictive Value PknotsRG: 0.701 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.643 MCFold: 0.522 Sensitivity PknotsRG: 0.580 MCFold: 0.535 Positive Predictive Value PknotsRG: 0.718 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.698 RDfolder: 0.592 Sensitivity PknotsRG: 0.626 RDfolder: 0.491 Positive Predictive Value PknotsRG: 0.787 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.501 RNAwolf: 0.332 Sensitivity PknotsRG: 0.443 RNAwolf: 0.309 Positive Predictive Value PknotsRG: 0.568 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.570 CMfinder(20): 0.546 Sensitivity PknotsRG: 0.494 CMfinder(20): 0.366 Positive Predictive Value PknotsRG: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.589 NanoFolder: 0.339 Sensitivity PknotsRG: 0.518 NanoFolder: 0.350 Positive Predictive Value PknotsRG: 0.675 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.558 PknotsRG: 0.557 Sensitivity Multilign(seed): 0.434 PknotsRG: 0.476 Positive Predictive Value Multilign(seed): 0.725 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.573 PPfold(seed): 0.092 Sensitivity PknotsRG: 0.496 PPfold(seed): 0.016 Positive Predictive Value PknotsRG: 0.669 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.588 RSpredict(seed): 0.266 Sensitivity PknotsRG: 0.533 RSpredict(seed): 0.128 Positive Predictive Value PknotsRG: 0.653 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.632 Carnac(seed): 0.241 Sensitivity PknotsRG: 0.568 Carnac(seed): 0.058 Positive Predictive Value PknotsRG: 0.708 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.591 Mastr(seed): 0.236 Sensitivity PknotsRG: 0.533 Mastr(seed): 0.062 Positive Predictive Value PknotsRG: 0.659 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 PknotsRG: 0.687 Sensitivity PETfold_2.0(seed): 0.642 PknotsRG: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 PknotsRG: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.647 PknotsRG: 0.549 Sensitivity PETfold_2.0(20): 0.509 PknotsRG: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 PknotsRG: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
ProbKnot	31 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.666 ProbKnot: 0.545 Sensitivity CentroidAlifold(20): 0.504 ProbKnot: 0.484 Positive Predictive Value CentroidAlifold(20): 0.883 ProbKnot: 0.619 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ProbKnot: 0.513 Sensitivity PETfold_pre2.0(seed): 0.602 ProbKnot: 0.447 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ProbKnot: 0.590 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	49 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.563 ProbKnot: 0.472 Sensitivity ContextFold: 0.466 ProbKnot: 0.414 Positive Predictive Value ContextFold: 0.681 ProbKnot: 0.539 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.654 ProbKnot: 0.550 Sensitivity MXScarna(seed): 0.548 ProbKnot: 0.493 Positive Predictive Value MXScarna(seed): 0.782 ProbKnot: 0.615 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.646 ProbKnot: 0.578 Sensitivity RNAalifold(20): 0.488 ProbKnot: 0.516 Positive Predictive Value RNAalifold(20): 0.857 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ProbKnot: 0.484 Sensitivity PETfold_pre2.0(20): 0.530 ProbKnot: 0.424 Positive Predictive Value PETfold_pre2.0(20): 0.798 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.26497248087e-08	15 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.691 ProbKnot: 0.565 Sensitivity PPfold(20): 0.544 ProbKnot: 0.495 Positive Predictive Value PPfold(20): 0.881 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	57 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.554 ProbKnot: 0.480 Sensitivity IPknot: 0.448 ProbKnot: 0.422 Positive Predictive Value IPknot: 0.688 ProbKnot: 0.548 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 ProbKnot: 0.544 Sensitivity CentroidAlifold(seed): 0.448 ProbKnot: 0.486 Positive Predictive Value CentroidAlifold(seed): 0.890 ProbKnot: 0.611 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.613 ProbKnot: 0.578 Sensitivity RNASampler(20): 0.455 ProbKnot: 0.516 Positive Predictive Value RNASampler(20): 0.830 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.655 ProbKnot: 0.565 Sensitivity TurboFold(20): 0.529 ProbKnot: 0.495 Positive Predictive Value TurboFold(20): 0.816 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	24 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.623 ProbKnot: 0.578 Sensitivity MXScarna(20): 0.514 ProbKnot: 0.516 Positive Predictive Value MXScarna(20): 0.759 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.557 ProbKnot: 0.536 Sensitivity Sfold: 0.480 ProbKnot: 0.480 Positive Predictive Value Sfold: 0.649 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 ProbKnot: 0.562 Sensitivity CentroidHomfold‑LAST: 0.439 ProbKnot: 0.497 Positive Predictive Value CentroidHomfold‑LAST: 0.789 ProbKnot: 0.641 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.547 ProbKnot: 0.536 Sensitivity Contrafold: 0.482 ProbKnot: 0.480 Positive Predictive Value Contrafold: 0.623 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 1.27481660653e-07	23 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.606 ProbKnot: 0.511 Sensitivity RNAalifold(seed): 0.435 ProbKnot: 0.459 Positive Predictive Value RNAalifold(seed): 0.845 ProbKnot: 0.571 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	91 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.606 ProbKnot: 0.594 Sensitivity HotKnots: 0.546 ProbKnot: 0.537 Positive Predictive Value HotKnots: 0.676 ProbKnot: 0.661 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 9.49173053431e-08	93 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.541 ProbKnot: 0.536 Sensitivity MaxExpect: 0.476 ProbKnot: 0.480 Positive Predictive Value MaxExpect: 0.616 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.541 ProbKnot: 0.532 Sensitivity CentroidFold: 0.450 ProbKnot: 0.475 Positive Predictive Value CentroidFold: 0.652 ProbKnot: 0.597 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 4.32815307575e-07	93 UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.537 ProbKnot: 0.536 Sensitivity UNAFold: 0.478 ProbKnot: 0.480 Positive Predictive Value UNAFold: 0.605 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.206416030449	92 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.548 ProbKnot: 0.544 Sensitivity PknotsRG: 0.493 ProbKnot: 0.490 Positive Predictive Value PknotsRG: 0.611 ProbKnot: 0.606 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 9.69999390915e-05		+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.578 Murlet(20): 0.570 Sensitivity ProbKnot: 0.516 Murlet(20): 0.415 Positive Predictive Value ProbKnot: 0.653 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 2.16681265449e-06	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.536 RNAfold: 0.535 Sensitivity ProbKnot: 0.480 RNAfold: 0.478 Positive Predictive Value ProbKnot: 0.601 RNAfold: 0.600 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.000609097173132	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.578 Carnac(20): 0.557 Sensitivity ProbKnot: 0.516 Carnac(20): 0.348 Positive Predictive Value ProbKnot: 0.653 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.48688953717e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.594 RNAshapes: 0.588 Sensitivity ProbKnot: 0.537 RNAshapes: 0.523 Positive Predictive Value ProbKnot: 0.661 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 9.69999390915e-05	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.536 Fold: 0.519 Sensitivity ProbKnot: 0.480 Fold: 0.466 Positive Predictive Value ProbKnot: 0.601 Fold: 0.579 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.544 ProbKnot: 0.499 Sensitivity TurboFold(seed): 0.439 ProbKnot: 0.437 Positive Predictive Value TurboFold(seed): 0.679 ProbKnot: 0.577 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.546 RSpredict(20): 0.529 Sensitivity ProbKnot: 0.486 RSpredict(20): 0.409 Positive Predictive Value ProbKnot: 0.617 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.535 Afold: 0.521 Sensitivity ProbKnot: 0.491 Afold: 0.479 Positive Predictive Value ProbKnot: 0.584 Afold: 0.568 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.594 RNAsubopt: 0.588 Sensitivity ProbKnot: 0.537 RNAsubopt: 0.530 Positive Predictive Value ProbKnot: 0.661 RNAsubopt: 0.657 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 1.83595875043e-07	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.530 RNASLOpt: 0.489 Sensitivity ProbKnot: 0.467 RNASLOpt: 0.393 Positive Predictive Value ProbKnot: 0.607 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.641 Cylofold: 0.603 Sensitivity ProbKnot: 0.580 Cylofold: 0.513 Positive Predictive Value ProbKnot: 0.715 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.535 McQFold: 0.482 Sensitivity ProbKnot: 0.478 McQFold: 0.416 Positive Predictive Value ProbKnot: 0.599 McQFold: 0.559 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.561 ProbKnot: 0.556 Sensitivity Multilign(20): 0.466 ProbKnot: 0.493 Positive Predictive Value Multilign(20): 0.682 ProbKnot: 0.634 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.83239157526e-05	- CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.585 ProbKnot: 0.580 Sensitivity CRWrnafold: 0.522 ProbKnot: 0.531 Positive Predictive Value CRWrnafold: 0.663 ProbKnot: 0.640 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.91710725109e-05	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.656 Pknots: 0.598 Sensitivity ProbKnot: 0.595 Pknots: 0.542 Positive Predictive Value ProbKnot: 0.728 Pknots: 0.667 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.560 RNASampler(seed): 0.528 Sensitivity ProbKnot: 0.526 RNASampler(seed): 0.375 Positive Predictive Value ProbKnot: 0.602 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.63443860185e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.723 Alterna: 0.688 Sensitivity ProbKnot: 0.671 Alterna: 0.630 Positive Predictive Value ProbKnot: 0.785 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.578 Mastr(20): 0.485 Sensitivity ProbKnot: 0.516 Mastr(20): 0.303 Positive Predictive Value ProbKnot: 0.653 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.628 Vsfold4: 0.528 Sensitivity ProbKnot: 0.575 Vsfold4: 0.450 Positive Predictive Value ProbKnot: 0.691 Vsfold4: 0.625 Number of pairs reference - predicted secondary structure: 85 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.550 Murlet(seed): 0.471 Sensitivity ProbKnot: 0.496 Murlet(seed): 0.271 Positive Predictive Value ProbKnot: 0.616 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.619 Vsfold5: 0.492 Sensitivity ProbKnot: 0.566 Vsfold5: 0.427 Positive Predictive Value ProbKnot: 0.681 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.620 MCFold: 0.509 Sensitivity ProbKnot: 0.564 MCFold: 0.521 Positive Predictive Value ProbKnot: 0.687 MCFold: 0.505 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.708 RDfolder: 0.602 Sensitivity ProbKnot: 0.653 RDfolder: 0.506 Positive Predictive Value ProbKnot: 0.776 RDfolder: 0.726 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.482 RNAwolf: 0.356 Sensitivity ProbKnot: 0.423 RNAwolf: 0.331 Positive Predictive Value ProbKnot: 0.549 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.582 CMfinder(20): 0.546 Sensitivity ProbKnot: 0.494 CMfinder(20): 0.366 Positive Predictive Value ProbKnot: 0.692 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.589 NanoFolder: 0.339 Sensitivity ProbKnot: 0.527 NanoFolder: 0.350 Positive Predictive Value ProbKnot: 0.664 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.564 Multilign(seed): 0.558 Sensitivity ProbKnot: 0.479 Multilign(seed): 0.434 Positive Predictive Value ProbKnot: 0.672 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.547 PPfold(seed): 0.092 Sensitivity ProbKnot: 0.478 PPfold(seed): 0.016 Positive Predictive Value ProbKnot: 0.632 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.545 RSpredict(seed): 0.356 Sensitivity ProbKnot: 0.487 RSpredict(seed): 0.208 Positive Predictive Value ProbKnot: 0.610 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.546 Carnac(seed): 0.412 Sensitivity ProbKnot: 0.483 Carnac(seed): 0.191 Positive Predictive Value ProbKnot: 0.619 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.573 Mastr(seed): 0.186 Sensitivity ProbKnot: 0.523 Mastr(seed): 0.035 Positive Predictive Value ProbKnot: 0.633 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 ProbKnot: 0.675 Sensitivity PETfold_2.0(seed): 0.642 ProbKnot: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 ProbKnot: 0.806 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 ProbKnot: 0.527 Sensitivity PETfold_2.0(20): 0.509 ProbKnot: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Murlet(20)	39 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Murlet(20): 0.582 Sensitivity CentroidAlifold(20): 0.516 Murlet(20): 0.430 Positive Predictive Value CentroidAlifold(20): 0.879 Murlet(20): 0.793 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(seed): 0.597 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	11 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.660 Murlet(20): 0.532 Sensitivity ContextFold: 0.525 Murlet(20): 0.394 Positive Predictive Value ContextFold: 0.835 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	33 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Murlet(20): 0.577 Sensitivity MXScarna(seed): 0.545 Murlet(20): 0.425 Positive Predictive Value MXScarna(seed): 0.801 Murlet(20): 0.788 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Murlet(20): 0.577 Sensitivity RNAalifold(20): 0.502 Murlet(20): 0.423 Positive Predictive Value RNAalifold(20): 0.860 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(20): 0.530 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.798 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	15 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.691 Murlet(20): 0.567 Sensitivity PPfold(20): 0.544 Murlet(20): 0.431 Positive Predictive Value PPfold(20): 0.881 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	14 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.601 Murlet(20): 0.569 Sensitivity IPknot: 0.485 Murlet(20): 0.428 Positive Predictive Value IPknot: 0.751 Murlet(20): 0.762 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	39 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Murlet(20): 0.582 Sensitivity CentroidAlifold(seed): 0.379 Murlet(20): 0.430 Positive Predictive Value CentroidAlifold(seed): 0.920 Murlet(20): 0.793 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 1.70900654697e-06	34 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Murlet(20): 0.577 Sensitivity RNASampler(20): 0.470 Murlet(20): 0.423 Positive Predictive Value RNASampler(20): 0.830 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Murlet(20): 0.567 Sensitivity TurboFold(20): 0.529 Murlet(20): 0.431 Positive Predictive Value TurboFold(20): 0.816 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	34 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Murlet(20): 0.577 Sensitivity MXScarna(20): 0.518 Murlet(20): 0.423 Positive Predictive Value MXScarna(20): 0.756 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.587 Murlet(20): 0.577 Sensitivity Sfold: 0.490 Murlet(20): 0.423 Positive Predictive Value Sfold: 0.708 Murlet(20): 0.791 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.34513818976e-06	14 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Murlet(20): 0.590 Sensitivity CentroidHomfold‑LAST: 0.549 Murlet(20): 0.453 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Murlet(20): 0.774 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	34 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.577 Contrafold: 0.551 Sensitivity Murlet(20): 0.423 Contrafold: 0.486 Positive Predictive Value Murlet(20): 0.791 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Murlet(20): 0.497 Sensitivity RNAalifold(seed): 0.351 Murlet(20): 0.340 Positive Predictive Value RNAalifold(seed): 0.930 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	34 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.577 HotKnots: 0.556 Sensitivity Murlet(20): 0.423 HotKnots: 0.495 Positive Predictive Value Murlet(20): 0.791 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.580 Murlet(20): 0.576 Sensitivity MaxExpect: 0.503 Murlet(20): 0.424 Positive Predictive Value MaxExpect: 0.674 Murlet(20): 0.786 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.000609097173132	39 Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.582 CentroidFold: 0.537 Sensitivity Murlet(20): 0.430 CentroidFold: 0.456 Positive Predictive Value Murlet(20): 0.793 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.577 UNAFold: 0.572 Sensitivity Murlet(20): 0.423 UNAFold: 0.501 Positive Predictive Value Murlet(20): 0.791 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0223116232526	34 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.577 PknotsRG: 0.572 Sensitivity Murlet(20): 0.423 PknotsRG: 0.508 Positive Predictive Value Murlet(20): 0.791 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.00353686086758	24 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.578 Murlet(20): 0.570 Sensitivity ProbKnot: 0.516 Murlet(20): 0.415 Positive Predictive Value ProbKnot: 0.653 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 2.16681265449e-06		+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.577 RNAfold: 0.562 Sensitivity Murlet(20): 0.423 RNAfold: 0.497 Positive Predictive Value Murlet(20): 0.791 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.82781450476e-07	= Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.577 Carnac(20): 0.577 Sensitivity Murlet(20): 0.423 Carnac(20): 0.372 Positive Predictive Value Murlet(20): 0.791 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0466667757771	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.577 RNAshapes: 0.567 Sensitivity Murlet(20): 0.423 RNAshapes: 0.498 Positive Predictive Value Murlet(20): 0.791 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.75845522374e-05	- Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.589 Murlet(20): 0.570 Sensitivity Fold: 0.525 Murlet(20): 0.415 Positive Predictive Value Fold: 0.664 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.59469103578e-08	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Murlet(20): 0.521 Sensitivity TurboFold(seed): 0.454 Murlet(20): 0.384 Positive Predictive Value TurboFold(seed): 0.708 Murlet(20): 0.712 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.581 RSpredict(20): 0.544 Sensitivity Murlet(20): 0.431 RSpredict(20): 0.425 Positive Predictive Value Murlet(20): 0.789 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.558 Afold: 0.530 Sensitivity Murlet(20): 0.408 Afold: 0.478 Positive Predictive Value Murlet(20): 0.766 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.15842348871e-07	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.577 RNAsubopt: 0.549 Sensitivity Murlet(20): 0.423 RNAsubopt: 0.490 Positive Predictive Value Murlet(20): 0.791 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Murlet(20): 0.532 Sensitivity RNASLOpt: 0.443 Murlet(20): 0.394 Positive Predictive Value RNASLOpt: 0.664 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0291093487101	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.638 Cylofold: 0.616 Sensitivity Murlet(20): 0.481 Cylofold: 0.528 Positive Predictive Value Murlet(20): 0.851 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.577 McQFold: 0.539 Sensitivity Murlet(20): 0.423 McQFold: 0.462 Positive Predictive Value Murlet(20): 0.791 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.576 Multilign(20): 0.561 Sensitivity Murlet(20): 0.430 Multilign(20): 0.466 Positive Predictive Value Murlet(20): 0.780 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.88034995625e-07	? Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.568 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.428 CRWrnafold: 0.483 Positive Predictive Value Murlet(20): 0.759 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.594 Pknots: 0.514 Sensitivity Murlet(20): 0.443 Pknots: 0.467 Positive Predictive Value Murlet(20): 0.801 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Murlet(20): 0.470 Sensitivity RNASampler(seed): 0.399 Murlet(20): 0.357 Positive Predictive Value RNASampler(seed): 0.739 Murlet(20): 0.623 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.658 Alterna: 0.571 Sensitivity Murlet(20): 0.510 Alterna: 0.504 Positive Predictive Value Murlet(20): 0.856 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.577 Mastr(20): 0.514 Sensitivity Murlet(20): 0.423 Mastr(20): 0.339 Positive Predictive Value Murlet(20): 0.791 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.586 Vsfold4: 0.477 Sensitivity Murlet(20): 0.431 Vsfold4: 0.401 Positive Predictive Value Murlet(20): 0.801 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.515 Murlet(seed): 0.463 Sensitivity Murlet(20): 0.359 Murlet(seed): 0.250 Positive Predictive Value Murlet(20): 0.744 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.586 Vsfold5: 0.417 Sensitivity Murlet(20): 0.431 Vsfold5: 0.355 Positive Predictive Value Murlet(20): 0.801 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.592 MCFold: 0.401 Sensitivity Murlet(20): 0.448 MCFold: 0.418 Positive Predictive Value Murlet(20): 0.789 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.646 RDfolder: 0.541 Sensitivity Murlet(20): 0.488 RDfolder: 0.440 Positive Predictive Value Murlet(20): 0.862 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.583 RNAwolf: 0.348 Sensitivity Murlet(20): 0.437 RNAwolf: 0.328 Positive Predictive Value Murlet(20): 0.784 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.600 CMfinder(20): 0.546 Sensitivity Murlet(20): 0.463 CMfinder(20): 0.366 Positive Predictive Value Murlet(20): 0.784 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.605 NanoFolder: 0.276 Sensitivity Murlet(20): 0.462 NanoFolder: 0.286 Positive Predictive Value Murlet(20): 0.797 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Murlet(20): 0.586 Sensitivity Multilign(seed): 0.468 Murlet(20): 0.447 Positive Predictive Value Multilign(seed): 0.795 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.569 PPfold(seed): 0.061 Sensitivity Murlet(20): 0.428 PPfold(seed): 0.010 Positive Predictive Value Murlet(20): 0.762 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.581 RSpredict(seed): 0.191 Sensitivity Murlet(20): 0.431 RSpredict(seed): 0.079 Positive Predictive Value Murlet(20): 0.789 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.557 Carnac(seed): 0.186 Sensitivity Murlet(20): 0.401 Carnac(seed): 0.035 Positive Predictive Value Murlet(20): 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.577 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.423 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.791 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Murlet(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(seed): 0.946 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Murlet(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAfold	39 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAfold: 0.538 Sensitivity CentroidAlifold(20): 0.516 RNAfold: 0.480 Positive Predictive Value CentroidAlifold(20): 0.879 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAfold: 0.500 Sensitivity PETfold_pre2.0(seed): 0.602 RNAfold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAfold: 0.573 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	49 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.563 RNAfold: 0.470 Sensitivity ContextFold: 0.466 RNAfold: 0.413 Positive Predictive Value ContextFold: 0.681 RNAfold: 0.535 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.667 RNAfold: 0.561 Sensitivity MXScarna(seed): 0.560 RNAfold: 0.502 Positive Predictive Value MXScarna(seed): 0.794 RNAfold: 0.627 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAfold: 0.562 Sensitivity RNAalifold(20): 0.502 RNAfold: 0.497 Positive Predictive Value RNAalifold(20): 0.860 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAfold: 0.483 Sensitivity PETfold_pre2.0(20): 0.530 RNAfold: 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	15 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.691 RNAfold: 0.565 Sensitivity PPfold(20): 0.544 RNAfold: 0.491 Positive Predictive Value PPfold(20): 0.881 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.74172190343e-08	57 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.554 RNAfold: 0.480 Sensitivity IPknot: 0.448 RNAfold: 0.422 Positive Predictive Value IPknot: 0.688 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 RNAfold: 0.553 Sensitivity CentroidAlifold(seed): 0.443 RNAfold: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.880 RNAfold: 0.620 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.623 RNAfold: 0.562 Sensitivity RNASampler(20): 0.470 RNAfold: 0.497 Positive Predictive Value RNASampler(20): 0.830 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.655 RNAfold: 0.565 Sensitivity TurboFold(20): 0.529 RNAfold: 0.491 Positive Predictive Value TurboFold(20): 0.816 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	34 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.624 RNAfold: 0.562 Sensitivity MXScarna(20): 0.518 RNAfold: 0.497 Positive Predictive Value MXScarna(20): 0.756 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.508 RNAfold: 0.484 Sensitivity Sfold: 0.432 RNAfold: 0.434 Positive Predictive Value Sfold: 0.599 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAfold: 0.585 Sensitivity CentroidHomfold‑LAST: 0.439 RNAfold: 0.508 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAfold: 0.677 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.647668092439	140 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.542 RNAfold: 0.484 Sensitivity Contrafold: 0.477 RNAfold: 0.434 Positive Predictive Value Contrafold: 0.616 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.631 RNAfold: 0.549 Sensitivity RNAalifold(seed): 0.460 RNAfold: 0.493 Positive Predictive Value RNAalifold(seed): 0.866 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.62644058675e-08	135 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.622 RNAfold: 0.613 Sensitivity HotKnots: 0.558 RNAfold: 0.547 Positive Predictive Value HotKnots: 0.699 RNAfold: 0.691 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.85233844192e-08	118 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.552 RNAfold: 0.519 Sensitivity MaxExpect: 0.480 RNAfold: 0.459 Positive Predictive Value MaxExpect: 0.635 RNAfold: 0.587 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.529 RNAfold: 0.492 Sensitivity CentroidFold: 0.442 RNAfold: 0.445 Positive Predictive Value CentroidFold: 0.634 RNAfold: 0.546 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.489 RNAfold: 0.484 Sensitivity UNAFold: 0.434 RNAfold: 0.434 Positive Predictive Value UNAFold: 0.550 RNAfold: 0.541 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.486 PknotsRG: 0.478 Sensitivity RNAfold: 0.436 PknotsRG: 0.430 Positive Predictive Value RNAfold: 0.542 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.536 RNAfold: 0.535 Sensitivity ProbKnot: 0.480 RNAfold: 0.478 Positive Predictive Value ProbKnot: 0.601 RNAfold: 0.600 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.000609097173132	34 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.577 RNAfold: 0.562 Sensitivity Murlet(20): 0.423 RNAfold: 0.497 Positive Predictive Value Murlet(20): 0.791 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.82781450476e-07		- Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.577 RNAfold: 0.562 Sensitivity Carnac(20): 0.372 RNAfold: 0.497 Positive Predictive Value Carnac(20): 0.897 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.70738736246e-07	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.613 RNAshapes: 0.602 Sensitivity RNAfold: 0.547 RNAshapes: 0.533 Positive Predictive Value RNAfold: 0.691 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.546 Fold: 0.535 Sensitivity RNAfold: 0.489 Fold: 0.481 Positive Predictive Value RNAfold: 0.611 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.85233844192e-08	- TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAfold: 0.525 Sensitivity TurboFold(seed): 0.439 RNAfold: 0.456 Positive Predictive Value TurboFold(seed): 0.679 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.89857672583e-08	= RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.544 RNAfold: 0.542 Sensitivity RSpredict(20): 0.425 RNAfold: 0.484 Positive Predictive Value RSpredict(20): 0.701 RNAfold: 0.610 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.150371979191	= Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.468 RNAfold: 0.468 Sensitivity Afold: 0.425 RNAfold: 0.424 Positive Predictive Value Afold: 0.517 RNAfold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.360712528037	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.613 RNAsubopt: 0.595 Sensitivity RNAfold: 0.547 RNAsubopt: 0.534 Positive Predictive Value RNAfold: 0.691 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.541 RNASLOpt: 0.489 Sensitivity RNAfold: 0.472 RNASLOpt: 0.393 Positive Predictive Value RNAfold: 0.624 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.636 Cylofold: 0.607 Sensitivity RNAfold: 0.566 Cylofold: 0.517 Positive Predictive Value RNAfold: 0.721 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.483 McQFold: 0.415 Sensitivity RNAfold: 0.433 McQFold: 0.332 Positive Predictive Value RNAfold: 0.540 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.580 Multilign(20): 0.561 Sensitivity RNAfold: 0.505 Multilign(20): 0.466 Positive Predictive Value RNAfold: 0.672 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.610 CRWrnafold: 0.585 Sensitivity RNAfold: 0.545 CRWrnafold: 0.522 Positive Predictive Value RNAfold: 0.691 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 8.81311508309e-08	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.650 Pknots: 0.601 Sensitivity RNAfold: 0.580 Pknots: 0.545 Positive Predictive Value RNAfold: 0.733 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.657 RNASampler(seed): 0.635 Sensitivity RNAfold: 0.604 RNASampler(seed): 0.484 Positive Predictive Value RNAfold: 0.719 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.709 Alterna: 0.665 Sensitivity RNAfold: 0.633 Alterna: 0.599 Positive Predictive Value RNAfold: 0.801 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.562 Mastr(20): 0.514 Sensitivity RNAfold: 0.497 Mastr(20): 0.339 Positive Predictive Value RNAfold: 0.640 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.633 Vsfold4: 0.547 Sensitivity RNAfold: 0.568 Vsfold4: 0.465 Positive Predictive Value RNAfold: 0.711 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.631 Murlet(seed): 0.514 Sensitivity RNAfold: 0.561 Murlet(seed): 0.315 Positive Predictive Value RNAfold: 0.715 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.630 Vsfold5: 0.510 Sensitivity RNAfold: 0.565 Vsfold5: 0.441 Positive Predictive Value RNAfold: 0.707 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.641 MCFold: 0.522 Sensitivity RNAfold: 0.577 MCFold: 0.535 Positive Predictive Value RNAfold: 0.718 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.697 RDfolder: 0.592 Sensitivity RNAfold: 0.623 RDfolder: 0.491 Positive Predictive Value RNAfold: 0.788 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.485 RNAwolf: 0.356 Sensitivity RNAfold: 0.427 RNAwolf: 0.331 Positive Predictive Value RNAfold: 0.552 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.570 CMfinder(20): 0.546 Sensitivity RNAfold: 0.494 CMfinder(20): 0.366 Positive Predictive Value RNAfold: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.590 NanoFolder: 0.339 Sensitivity RNAfold: 0.518 NanoFolder: 0.350 Positive Predictive Value RNAfold: 0.677 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.558 RNAfold: 0.555 Sensitivity Multilign(seed): 0.434 RNAfold: 0.476 Positive Predictive Value Multilign(seed): 0.725 RNAfold: 0.654 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.552 PPfold(seed): 0.092 Sensitivity RNAfold: 0.475 PPfold(seed): 0.016 Positive Predictive Value RNAfold: 0.648 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.555 RSpredict(seed): 0.375 Sensitivity RNAfold: 0.498 RSpredict(seed): 0.220 Positive Predictive Value RNAfold: 0.621 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.571 Carnac(seed): 0.404 Sensitivity RNAfold: 0.507 Carnac(seed): 0.181 Positive Predictive Value RNAfold: 0.645 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.590 Mastr(seed): 0.236 Sensitivity RNAfold: 0.531 Mastr(seed): 0.062 Positive Predictive Value RNAfold: 0.660 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAfold: 0.682 Sensitivity PETfold_2.0(seed): 0.642 RNAfold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAfold: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAfold: 0.541 Sensitivity PETfold_2.0(20): 0.509 RNAfold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 RNAfold: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Carnac(20)	39 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Carnac(20): 0.579 Sensitivity CentroidAlifold(20): 0.516 Carnac(20): 0.374 Positive Predictive Value CentroidAlifold(20): 0.879 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(seed): 0.597 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	11 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.660 Carnac(20): 0.524 Sensitivity ContextFold: 0.525 Carnac(20): 0.337 Positive Predictive Value ContextFold: 0.835 Carnac(20): 0.820 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	33 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Carnac(20): 0.580 Sensitivity MXScarna(seed): 0.545 Carnac(20): 0.377 Positive Predictive Value MXScarna(seed): 0.801 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Carnac(20): 0.577 Sensitivity RNAalifold(20): 0.502 Carnac(20): 0.372 Positive Predictive Value RNAalifold(20): 0.860 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(20): 0.530 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(20): 0.798 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64481516727e-08	15 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.691 Carnac(20): 0.547 Sensitivity PPfold(20): 0.544 Carnac(20): 0.357 Positive Predictive Value PPfold(20): 0.881 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	14 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.601 Carnac(20): 0.558 Sensitivity IPknot: 0.485 Carnac(20): 0.371 Positive Predictive Value IPknot: 0.751 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	39 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Carnac(20): 0.579 Sensitivity CentroidAlifold(seed): 0.379 Carnac(20): 0.374 Positive Predictive Value CentroidAlifold(seed): 0.920 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 9.291770879e-07	34 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Carnac(20): 0.577 Sensitivity RNASampler(20): 0.470 Carnac(20): 0.372 Positive Predictive Value RNASampler(20): 0.830 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Carnac(20): 0.547 Sensitivity TurboFold(20): 0.529 Carnac(20): 0.357 Positive Predictive Value TurboFold(20): 0.816 Carnac(20): 0.844 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	34 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Carnac(20): 0.577 Sensitivity MXScarna(20): 0.518 Carnac(20): 0.372 Positive Predictive Value MXScarna(20): 0.756 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.587 Carnac(20): 0.577 Sensitivity Sfold: 0.490 Carnac(20): 0.372 Positive Predictive Value Sfold: 0.708 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.10039559051e-07	14 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Carnac(20): 0.568 Sensitivity CentroidHomfold‑LAST: 0.549 Carnac(20): 0.382 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Carnac(20): 0.850 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	34 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.577 Contrafold: 0.551 Sensitivity Carnac(20): 0.372 Contrafold: 0.486 Positive Predictive Value Carnac(20): 0.897 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	20 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Carnac(20): 0.507 Sensitivity RNAalifold(seed): 0.351 Carnac(20): 0.275 Positive Predictive Value RNAalifold(seed): 0.930 Carnac(20): 0.939 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	34 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.577 HotKnots: 0.556 Sensitivity Carnac(20): 0.372 HotKnots: 0.495 Positive Predictive Value Carnac(20): 0.897 HotKnots: 0.628 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.580 Carnac(20): 0.578 Sensitivity MaxExpect: 0.503 Carnac(20): 0.375 Positive Predictive Value MaxExpect: 0.674 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.518809073978	39 Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.579 CentroidFold: 0.537 Sensitivity Carnac(20): 0.374 CentroidFold: 0.456 Positive Predictive Value Carnac(20): 0.899 CentroidFold: 0.637 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.577 UNAFold: 0.572 Sensitivity Carnac(20): 0.372 UNAFold: 0.501 Positive Predictive Value Carnac(20): 0.897 UNAFold: 0.658 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.000218715568349	34 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.577 PknotsRG: 0.572 Sensitivity Carnac(20): 0.372 PknotsRG: 0.508 Positive Predictive Value Carnac(20): 0.897 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.00353686086758	24 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.578 Carnac(20): 0.557 Sensitivity ProbKnot: 0.516 Carnac(20): 0.348 Positive Predictive Value ProbKnot: 0.653 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.48688953717e-08	34 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.577 Carnac(20): 0.577 Sensitivity Murlet(20): 0.423 Carnac(20): 0.372 Positive Predictive Value Murlet(20): 0.791 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0466667757771	34 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.577 RNAfold: 0.562 Sensitivity Carnac(20): 0.372 RNAfold: 0.497 Positive Predictive Value Carnac(20): 0.897 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.70738736246e-07		+ Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.577 RNAshapes: 0.567 Sensitivity Carnac(20): 0.372 RNAshapes: 0.498 Positive Predictive Value Carnac(20): 0.897 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.08735181805e-06	- Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.589 Carnac(20): 0.557 Sensitivity Fold: 0.525 Carnac(20): 0.348 Positive Predictive Value Fold: 0.664 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.38150542963e-08	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Carnac(20): 0.493 Sensitivity TurboFold(seed): 0.454 Carnac(20): 0.286 Positive Predictive Value TurboFold(seed): 0.708 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.580 RSpredict(20): 0.544 Sensitivity Carnac(20): 0.376 RSpredict(20): 0.425 Positive Predictive Value Carnac(20): 0.898 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.587 Afold: 0.530 Sensitivity Carnac(20): 0.372 Afold: 0.478 Positive Predictive Value Carnac(20): 0.929 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.577 RNAsubopt: 0.549 Sensitivity Carnac(20): 0.372 RNAsubopt: 0.490 Positive Predictive Value Carnac(20): 0.897 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Carnac(20): 0.524 Sensitivity RNASLOpt: 0.443 Carnac(20): 0.337 Positive Predictive Value RNASLOpt: 0.664 Carnac(20): 0.820 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.81657399344e-06	- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.616 Carnac(20): 0.593 Sensitivity Cylofold: 0.528 Carnac(20): 0.392 Positive Predictive Value Cylofold: 0.725 Carnac(20): 0.902 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.577 McQFold: 0.539 Sensitivity Carnac(20): 0.372 McQFold: 0.462 Positive Predictive Value Carnac(20): 0.897 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.561 Carnac(20): 0.549 Sensitivity Multilign(20): 0.466 Carnac(20): 0.356 Positive Predictive Value Multilign(20): 0.682 Carnac(20): 0.853 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.76858620702e-06	? CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Carnac(20): 0.526 Sensitivity CRWrnafold: 0.483 Carnac(20): 0.335 Positive Predictive Value CRWrnafold: 0.623 Carnac(20): 0.832 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.587 Pknots: 0.514 Sensitivity Carnac(20): 0.388 Pknots: 0.467 Positive Predictive Value Carnac(20): 0.894 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Carnac(20): 0.534 Sensitivity RNASampler(seed): 0.399 Carnac(20): 0.306 Positive Predictive Value RNASampler(seed): 0.739 Carnac(20): 0.937 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.662 Alterna: 0.571 Sensitivity Carnac(20): 0.477 Alterna: 0.504 Positive Predictive Value Carnac(20): 0.925 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.577 Mastr(20): 0.514 Sensitivity Carnac(20): 0.372 Mastr(20): 0.339 Positive Predictive Value Carnac(20): 0.897 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.585 Vsfold4: 0.477 Sensitivity Carnac(20): 0.382 Vsfold4: 0.401 Positive Predictive Value Carnac(20): 0.900 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.514 Murlet(seed): 0.463 Sensitivity Carnac(20): 0.283 Murlet(seed): 0.250 Positive Predictive Value Carnac(20): 0.939 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.585 Vsfold5: 0.417 Sensitivity Carnac(20): 0.382 Vsfold5: 0.355 Positive Predictive Value Carnac(20): 0.900 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.592 MCFold: 0.401 Sensitivity Carnac(20): 0.393 MCFold: 0.418 Positive Predictive Value Carnac(20): 0.896 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.616 RDfolder: 0.541 Sensitivity Carnac(20): 0.429 RDfolder: 0.440 Positive Predictive Value Carnac(20): 0.890 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.565 RNAwolf: 0.348 Sensitivity Carnac(20): 0.371 RNAwolf: 0.328 Positive Predictive Value Carnac(20): 0.867 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.567 CMfinder(20): 0.546 Sensitivity Carnac(20): 0.402 CMfinder(20): 0.366 Positive Predictive Value Carnac(20): 0.805 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.574 NanoFolder: 0.276 Sensitivity Carnac(20): 0.396 NanoFolder: 0.286 Positive Predictive Value Carnac(20): 0.837 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Carnac(20): 0.507 Sensitivity Multilign(seed): 0.468 Carnac(20): 0.300 Positive Predictive Value Multilign(seed): 0.795 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.558 PPfold(seed): 0.061 Sensitivity Carnac(20): 0.371 PPfold(seed): 0.010 Positive Predictive Value Carnac(20): 0.844 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.580 RSpredict(seed): 0.191 Sensitivity Carnac(20): 0.376 RSpredict(seed): 0.079 Positive Predictive Value Carnac(20): 0.898 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.563 Carnac(seed): 0.186 Sensitivity Carnac(20): 0.345 Carnac(seed): 0.035 Positive Predictive Value Carnac(20): 0.926 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.577 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.372 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.897 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Carnac(20): 0.576 Sensitivity PETfold_2.0(seed): 0.614 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(seed): 0.946 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Carnac(20): 0.576 Sensitivity PETfold_2.0(20): 0.509 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(20): 0.829 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAshapes	39 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAshapes: 0.536 Sensitivity CentroidAlifold(20): 0.516 RNAshapes: 0.473 Positive Predictive Value CentroidAlifold(20): 0.879 RNAshapes: 0.612 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAshapes: 0.491 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAshapes: 0.567 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	47 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.633 RNAshapes: 0.512 Sensitivity ContextFold: 0.523 RNAshapes: 0.447 Positive Predictive Value ContextFold: 0.769 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.666 RNAshapes: 0.585 Sensitivity MXScarna(seed): 0.554 RNAshapes: 0.525 Positive Predictive Value MXScarna(seed): 0.804 RNAshapes: 0.657 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAshapes: 0.567 Sensitivity RNAalifold(20): 0.502 RNAshapes: 0.498 Positive Predictive Value RNAalifold(20): 0.860 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAshapes: 0.454 Sensitivity PETfold_pre2.0(20): 0.530 RNAshapes: 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	15 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.691 RNAshapes: 0.557 Sensitivity PPfold(20): 0.544 RNAshapes: 0.486 Positive Predictive Value PPfold(20): 0.881 RNAshapes: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	55 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.615 RNAshapes: 0.526 Sensitivity IPknot: 0.512 RNAshapes: 0.459 Positive Predictive Value IPknot: 0.742 RNAshapes: 0.609 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RNAshapes: 0.565 Sensitivity CentroidAlifold(seed): 0.397 RNAshapes: 0.505 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAshapes: 0.636 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.623 RNAshapes: 0.567 Sensitivity RNASampler(20): 0.470 RNAshapes: 0.498 Positive Predictive Value RNASampler(20): 0.830 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.655 RNAshapes: 0.557 Sensitivity TurboFold(20): 0.529 RNAshapes: 0.486 Positive Predictive Value TurboFold(20): 0.816 RNAshapes: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	34 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.624 RNAshapes: 0.567 Sensitivity MXScarna(20): 0.518 RNAshapes: 0.498 Positive Predictive Value MXScarna(20): 0.756 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.640 RNAshapes: 0.602 Sensitivity Sfold: 0.548 RNAshapes: 0.533 Positive Predictive Value Sfold: 0.751 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAshapes: 0.558 Sensitivity CentroidHomfold‑LAST: 0.439 RNAshapes: 0.483 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAshapes: 0.650 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.618 RNAshapes: 0.602 Sensitivity Contrafold: 0.550 RNAshapes: 0.533 Positive Predictive Value Contrafold: 0.700 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.596 RNAshapes: 0.595 Sensitivity RNAalifold(seed): 0.397 RNAshapes: 0.537 Positive Predictive Value RNAalifold(seed): 0.897 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 9.17559933998e-05	135 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.622 RNAshapes: 0.602 Sensitivity HotKnots: 0.558 RNAshapes: 0.533 Positive Predictive Value HotKnots: 0.699 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	115 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.610 RNAshapes: 0.600 Sensitivity MaxExpect: 0.539 RNAshapes: 0.533 Positive Predictive Value MaxExpect: 0.695 RNAshapes: 0.679 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 4.48494289621e-08	133 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.601 RNAshapes: 0.586 Sensitivity CentroidFold: 0.515 RNAshapes: 0.521 Positive Predictive Value CentroidFold: 0.706 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.624 RNAshapes: 0.602 Sensitivity UNAFold: 0.554 RNAshapes: 0.533 Positive Predictive Value UNAFold: 0.707 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.608 RNAshapes: 0.602 Sensitivity PknotsRG: 0.544 RNAshapes: 0.533 Positive Predictive Value PknotsRG: 0.683 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 6.53888633552e-08	91 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.594 RNAshapes: 0.588 Sensitivity ProbKnot: 0.537 RNAshapes: 0.523 Positive Predictive Value ProbKnot: 0.661 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 9.69999390915e-05	34 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.577 RNAshapes: 0.567 Sensitivity Murlet(20): 0.423 RNAshapes: 0.498 Positive Predictive Value Murlet(20): 0.791 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.75845522374e-05	135 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.613 RNAshapes: 0.602 Sensitivity RNAfold: 0.547 RNAshapes: 0.533 Positive Predictive Value RNAfold: 0.691 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.577 RNAshapes: 0.567 Sensitivity Carnac(20): 0.372 RNAshapes: 0.498 Positive Predictive Value Carnac(20): 0.897 RNAshapes: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.08735181805e-06		= RNAshapes vs Fold Matthews Correlation Coefficient RNAshapes: 0.605 Fold: 0.605 Sensitivity RNAshapes: 0.539 Fold: 0.544 Positive Predictive Value RNAshapes: 0.683 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.216235860451	- TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAshapes: 0.520 Sensitivity TurboFold(seed): 0.439 RNAshapes: 0.453 Positive Predictive Value TurboFold(seed): 0.679 RNAshapes: 0.604 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.92661845584e-08	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.551 RSpredict(20): 0.544 Sensitivity RNAshapes: 0.488 RSpredict(20): 0.425 Positive Predictive Value RNAshapes: 0.625 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 7.75845522374e-05	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.622 Afold: 0.615 Sensitivity RNAshapes: 0.561 Afold: 0.563 Positive Predictive Value RNAshapes: 0.694 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.39704516867e-06	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.602 RNAsubopt: 0.595 Sensitivity RNAshapes: 0.533 RNAsubopt: 0.534 Positive Predictive Value RNAshapes: 0.685 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.512 RNASLOpt: 0.489 Sensitivity RNAshapes: 0.447 RNASLOpt: 0.393 Positive Predictive Value RNAshapes: 0.593 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.639 Cylofold: 0.607 Sensitivity RNAshapes: 0.566 Cylofold: 0.517 Positive Predictive Value RNAshapes: 0.727 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.601 McQFold: 0.571 Sensitivity RNAshapes: 0.532 McQFold: 0.492 Positive Predictive Value RNAshapes: 0.683 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.624 Multilign(20): 0.561 Sensitivity RNAshapes: 0.543 Multilign(20): 0.466 Positive Predictive Value RNAshapes: 0.723 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.609 CRWrnafold: 0.585 Sensitivity RNAshapes: 0.542 CRWrnafold: 0.522 Positive Predictive Value RNAshapes: 0.691 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 6.54014656494e-08	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.645 Pknots: 0.601 Sensitivity RNAshapes: 0.573 Pknots: 0.545 Positive Predictive Value RNAshapes: 0.733 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.640 RNASampler(seed): 0.635 Sensitivity RNAshapes: 0.588 RNASampler(seed): 0.484 Positive Predictive Value RNAshapes: 0.702 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 7.17916828225e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.698 Alterna: 0.665 Sensitivity RNAshapes: 0.618 Alterna: 0.599 Positive Predictive Value RNAshapes: 0.796 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.567 Mastr(20): 0.514 Sensitivity RNAshapes: 0.498 Mastr(20): 0.339 Positive Predictive Value RNAshapes: 0.651 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.624 Vsfold4: 0.547 Sensitivity RNAshapes: 0.555 Vsfold4: 0.465 Positive Predictive Value RNAshapes: 0.706 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.640 Murlet(seed): 0.514 Sensitivity RNAshapes: 0.568 Murlet(seed): 0.315 Positive Predictive Value RNAshapes: 0.726 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.623 Vsfold5: 0.510 Sensitivity RNAshapes: 0.555 Vsfold5: 0.441 Positive Predictive Value RNAshapes: 0.706 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.638 MCFold: 0.522 Sensitivity RNAshapes: 0.571 MCFold: 0.535 Positive Predictive Value RNAshapes: 0.719 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.689 RDfolder: 0.592 Sensitivity RNAshapes: 0.609 RDfolder: 0.491 Positive Predictive Value RNAshapes: 0.786 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.517 RNAwolf: 0.385 Sensitivity RNAshapes: 0.452 RNAwolf: 0.360 Positive Predictive Value RNAshapes: 0.596 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: 0.556 CMfinder(20): 0.546 Sensitivity RNAshapes: 0.482 CMfinder(20): 0.366 Positive Predictive Value RNAshapes: 0.648 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.557 NanoFolder: 0.339 Sensitivity RNAshapes: 0.491 NanoFolder: 0.350 Positive Predictive Value RNAshapes: 0.640 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.558 RNAshapes: 0.548 Sensitivity Multilign(seed): 0.434 RNAshapes: 0.472 Positive Predictive Value Multilign(seed): 0.725 RNAshapes: 0.643 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.531 PPfold(seed): 0.092 Sensitivity RNAshapes: 0.458 PPfold(seed): 0.016 Positive Predictive Value RNAshapes: 0.622 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.575 RSpredict(seed): 0.266 Sensitivity RNAshapes: 0.516 RSpredict(seed): 0.128 Positive Predictive Value RNAshapes: 0.646 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.637 Carnac(seed): 0.241 Sensitivity RNAshapes: 0.569 Carnac(seed): 0.058 Positive Predictive Value RNAshapes: 0.719 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.580 Mastr(seed): 0.236 Sensitivity RNAshapes: 0.518 Mastr(seed): 0.062 Positive Predictive Value RNAshapes: 0.654 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAshapes: 0.493 Sensitivity PETfold_2.0(seed): 0.642 RNAshapes: 0.411 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAshapes: 0.600 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAshapes: 0.199 Sensitivity PETfold_2.0(20): 0.509 RNAshapes: 0.158 Positive Predictive Value PETfold_2.0(20): 0.829 RNAshapes: 0.265 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Fold	31 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.666 Fold: 0.552 Sensitivity CentroidAlifold(20): 0.504 Fold: 0.491 Positive Predictive Value CentroidAlifold(20): 0.883 Fold: 0.624 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Fold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.602 Fold: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Fold: 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	49 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.563 Fold: 0.436 Sensitivity ContextFold: 0.466 Fold: 0.388 Positive Predictive Value ContextFold: 0.681 Fold: 0.492 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.661 Fold: 0.563 Sensitivity MXScarna(seed): 0.556 Fold: 0.507 Positive Predictive Value MXScarna(seed): 0.787 Fold: 0.625 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.646 Fold: 0.589 Sensitivity RNAalifold(20): 0.488 Fold: 0.525 Positive Predictive Value RNAalifold(20): 0.857 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Fold: 0.458 Sensitivity PETfold_pre2.0(20): 0.530 Fold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 Fold: 0.521 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	15 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.691 Fold: 0.535 Sensitivity PPfold(20): 0.544 Fold: 0.473 Positive Predictive Value PPfold(20): 0.881 Fold: 0.611 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	57 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.554 Fold: 0.448 Sensitivity IPknot: 0.448 Fold: 0.398 Positive Predictive Value IPknot: 0.688 Fold: 0.505 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.628 Fold: 0.554 Sensitivity CentroidAlifold(seed): 0.449 Fold: 0.498 Positive Predictive Value CentroidAlifold(seed): 0.879 Fold: 0.618 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.613 Fold: 0.589 Sensitivity RNASampler(20): 0.455 Fold: 0.525 Positive Predictive Value RNASampler(20): 0.830 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	15 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.655 Fold: 0.535 Sensitivity TurboFold(20): 0.529 Fold: 0.473 Positive Predictive Value TurboFold(20): 0.816 Fold: 0.611 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.70887622364e-08	24 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.623 Fold: 0.589 Sensitivity MXScarna(20): 0.514 Fold: 0.525 Positive Predictive Value MXScarna(20): 0.759 Fold: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	101 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.570 Fold: 0.535 Sensitivity Sfold: 0.491 Fold: 0.481 Positive Predictive Value Sfold: 0.662 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 Fold: 0.537 Sensitivity CentroidHomfold‑LAST: 0.439 Fold: 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.789 Fold: 0.615 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.563 Fold: 0.535 Sensitivity Contrafold: 0.496 Fold: 0.481 Positive Predictive Value Contrafold: 0.640 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.626 Fold: 0.520 Sensitivity RNAalifold(seed): 0.457 Fold: 0.472 Positive Predictive Value RNAalifold(seed): 0.857 Fold: 0.573 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	99 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.623 Fold: 0.605 Sensitivity HotKnots: 0.562 Fold: 0.544 Positive Predictive Value HotKnots: 0.694 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 8.81311508309e-08	101 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.553 Fold: 0.535 Sensitivity MaxExpect: 0.487 Fold: 0.481 Positive Predictive Value MaxExpect: 0.628 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	113 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.556 Fold: 0.531 Sensitivity CentroidFold: 0.464 Fold: 0.476 Positive Predictive Value CentroidFold: 0.668 Fold: 0.593 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.553 Fold: 0.535 Sensitivity UNAFold: 0.492 Fold: 0.481 Positive Predictive Value UNAFold: 0.622 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 4.48494289621e-08	100 PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.558 Fold: 0.550 Sensitivity PknotsRG: 0.503 Fold: 0.495 Positive Predictive Value PknotsRG: 0.621 Fold: 0.613 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 5.5212650266e-05	93 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.536 Fold: 0.519 Sensitivity ProbKnot: 0.480 Fold: 0.466 Positive Predictive Value ProbKnot: 0.601 Fold: 0.579 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.589 Murlet(20): 0.570 Sensitivity Fold: 0.525 Murlet(20): 0.415 Positive Predictive Value Fold: 0.664 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.59469103578e-08	101 RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.546 Fold: 0.535 Sensitivity RNAfold: 0.489 Fold: 0.481 Positive Predictive Value RNAfold: 0.611 Fold: 0.597 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.85233844192e-08	24 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.589 Carnac(20): 0.557 Sensitivity Fold: 0.525 Carnac(20): 0.348 Positive Predictive Value Fold: 0.664 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.38150542963e-08	99 RNAshapes vs Fold Matthews Correlation Coefficient RNAshapes: 0.605 Fold: 0.605 Sensitivity RNAshapes: 0.539 Fold: 0.544 Positive Predictive Value RNAshapes: 0.683 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.216235860451		- TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.544 Fold: 0.447 Sensitivity TurboFold(seed): 0.439 Fold: 0.394 Positive Predictive Value TurboFold(seed): 0.679 Fold: 0.516 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.553 RSpredict(20): 0.529 Sensitivity Fold: 0.495 RSpredict(20): 0.409 Positive Predictive Value Fold: 0.624 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.18450348589e-07	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.560 Afold: 0.546 Sensitivity Fold: 0.514 Afold: 0.502 Positive Predictive Value Fold: 0.612 Afold: 0.594 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.85233844192e-08	= RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.605 Fold: 0.605 Sensitivity RNAsubopt: 0.546 Fold: 0.544 Positive Predictive Value RNAsubopt: 0.675 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.264581540075	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.496 RNASLOpt: 0.489 Sensitivity Fold: 0.438 RNASLOpt: 0.393 Positive Predictive Value Fold: 0.567 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 2.29562105844e-05	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.659 Cylofold: 0.607 Sensitivity Fold: 0.589 Cylofold: 0.517 Positive Predictive Value Fold: 0.742 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.533 McQFold: 0.495 Sensitivity Fold: 0.479 McQFold: 0.426 Positive Predictive Value Fold: 0.595 McQFold: 0.576 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.601 Multilign(20): 0.561 Sensitivity Fold: 0.530 Multilign(20): 0.466 Positive Predictive Value Fold: 0.688 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.70180496535e-08	- CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.585 Fold: 0.573 Sensitivity CRWrnafold: 0.522 Fold: 0.514 Positive Predictive Value CRWrnafold: 0.663 Fold: 0.645 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.679 Pknots: 0.611 Sensitivity Fold: 0.612 Pknots: 0.554 Positive Predictive Value Fold: 0.758 Pknots: 0.680 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.614 Fold: 0.608 Sensitivity RNASampler(seed): 0.461 Fold: 0.571 Positive Predictive Value RNASampler(seed): 0.822 Fold: 0.654 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00454636894862	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.751 Alterna: 0.698 Sensitivity Fold: 0.684 Alterna: 0.640 Positive Predictive Value Fold: 0.832 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.589 Mastr(20): 0.485 Sensitivity Fold: 0.525 Mastr(20): 0.303 Positive Predictive Value Fold: 0.664 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.656 Vsfold4: 0.550 Sensitivity Fold: 0.594 Vsfold4: 0.470 Positive Predictive Value Fold: 0.730 Vsfold4: 0.648 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.599 Murlet(seed): 0.509 Sensitivity Fold: 0.543 Murlet(seed): 0.310 Positive Predictive Value Fold: 0.665 Murlet(seed): 0.842 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.648 Vsfold5: 0.512 Sensitivity Fold: 0.586 Vsfold5: 0.445 Positive Predictive Value Fold: 0.720 Vsfold5: 0.595 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.639 MCFold: 0.526 Sensitivity Fold: 0.579 MCFold: 0.538 Positive Predictive Value Fold: 0.711 MCFold: 0.522 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.726 RDfolder: 0.614 Sensitivity Fold: 0.658 RDfolder: 0.517 Positive Predictive Value Fold: 0.808 RDfolder: 0.740 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.452 RNAwolf: 0.356 Sensitivity Fold: 0.402 RNAwolf: 0.331 Positive Predictive Value Fold: 0.511 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.556 CMfinder(20): 0.546 Sensitivity Fold: 0.488 CMfinder(20): 0.366 Positive Predictive Value Fold: 0.640 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.609 NanoFolder: 0.339 Sensitivity Fold: 0.537 NanoFolder: 0.350 Positive Predictive Value Fold: 0.696 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.558 Fold: 0.522 Sensitivity Multilign(seed): 0.434 Fold: 0.455 Positive Predictive Value Multilign(seed): 0.725 Fold: 0.607 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.532 PPfold(seed): 0.092 Sensitivity Fold: 0.466 PPfold(seed): 0.016 Positive Predictive Value Fold: 0.615 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.555 RSpredict(seed): 0.373 Sensitivity Fold: 0.500 RSpredict(seed): 0.222 Positive Predictive Value Fold: 0.618 RSpredict(seed): 0.631 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.548 Carnac(seed): 0.426 Sensitivity Fold: 0.492 Carnac(seed): 0.202 Positive Predictive Value Fold: 0.611 Carnac(seed): 0.900 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.609 Mastr(seed): 0.247 Sensitivity Fold: 0.552 Mastr(seed): 0.069 Positive Predictive Value Fold: 0.676 Mastr(seed): 0.886 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Fold: 0.665 Sensitivity PETfold_2.0(seed): 0.642 Fold: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 Fold: 0.783 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Fold: 0.513 Sensitivity PETfold_2.0(20): 0.509 Fold: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 Fold: 0.632 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
TurboFold(seed)	11 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.569 TurboFold(seed): 0.510 Sensitivity CentroidAlifold(20): 0.391 TurboFold(seed): 0.419 Positive Predictive Value CentroidAlifold(20): 0.833 TurboFold(seed): 0.626 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	12 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.645 TurboFold(seed): 0.504 Sensitivity PETfold_pre2.0(seed): 0.511 TurboFold(seed): 0.416 Positive Predictive Value PETfold_pre2.0(seed): 0.818 TurboFold(seed): 0.616 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	8 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.508 TurboFold(seed): 0.478 Sensitivity ContextFold: 0.396 TurboFold(seed): 0.382 Positive Predictive Value ContextFold: 0.657 TurboFold(seed): 0.603 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.548 TurboFold(seed): 0.544 Sensitivity MXScarna(seed): 0.429 TurboFold(seed): 0.439 Positive Predictive Value MXScarna(seed): 0.707 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0173590247318	9 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 RNAalifold(20): 0.561 Sensitivity TurboFold(seed): 0.454 RNAalifold(20): 0.425 Positive Predictive Value TurboFold(seed): 0.708 RNAalifold(20): 0.744 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.488 TurboFold(seed): 0.437 Sensitivity PETfold_pre2.0(20): 0.375 TurboFold(seed): 0.358 Positive Predictive Value PETfold_pre2.0(20): 0.639 TurboFold(seed): 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.596 TurboFold(seed): 0.565 Sensitivity PPfold(20): 0.444 TurboFold(seed): 0.454 Positive Predictive Value PPfold(20): 0.805 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.542 TurboFold(seed): 0.518 Sensitivity IPknot: 0.416 TurboFold(seed): 0.413 Positive Predictive Value IPknot: 0.712 TurboFold(seed): 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.59581922198e-08	15 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 TurboFold(seed): 0.547 Sensitivity CentroidAlifold(seed): 0.401 TurboFold(seed): 0.452 Positive Predictive Value CentroidAlifold(seed): 0.927 TurboFold(seed): 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	9 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.584 TurboFold(seed): 0.565 Sensitivity RNASampler(20): 0.438 TurboFold(seed): 0.454 Positive Predictive Value RNASampler(20): 0.784 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.578 TurboFold(seed): 0.565 Sensitivity TurboFold(20): 0.454 TurboFold(seed): 0.454 Positive Predictive Value TurboFold(20): 0.741 TurboFold(seed): 0.708 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 MXScarna(20): 0.532 Sensitivity TurboFold(seed): 0.454 MXScarna(20): 0.422 Positive Predictive Value TurboFold(seed): 0.708 MXScarna(20): 0.675 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.559 TurboFold(seed): 0.544 Sensitivity Sfold: 0.439 TurboFold(seed): 0.439 Positive Predictive Value Sfold: 0.718 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.50659327008e-08	10 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.566 CentroidHomfold‑LAST: 0.556 Sensitivity TurboFold(seed): 0.467 CentroidHomfold‑LAST: 0.461 Positive Predictive Value TurboFold(seed): 0.693 CentroidHomfold‑LAST: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.63118549175e-06	11 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.544 Contrafold: 0.544 Sensitivity TurboFold(seed): 0.439 Contrafold: 0.456 Positive Predictive Value TurboFold(seed): 0.679 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0195049618507	10 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.532 TurboFold(seed): 0.518 Sensitivity RNAalifold(seed): 0.341 TurboFold(seed): 0.416 Positive Predictive Value RNAalifold(seed): 0.837 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0168018190577	11 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.544 HotKnots: 0.523 Sensitivity TurboFold(seed): 0.439 HotKnots: 0.464 Positive Predictive Value TurboFold(seed): 0.679 HotKnots: 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0017676675921	11 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.544 MaxExpect: 0.506 Sensitivity TurboFold(seed): 0.439 MaxExpect: 0.418 Positive Predictive Value TurboFold(seed): 0.679 MaxExpect: 0.620 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	15 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.547 CentroidFold: 0.514 Sensitivity TurboFold(seed): 0.452 CentroidFold: 0.413 Positive Predictive Value TurboFold(seed): 0.667 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	11 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.544 UNAFold: 0.484 Sensitivity TurboFold(seed): 0.439 UNAFold: 0.418 Positive Predictive Value TurboFold(seed): 0.679 UNAFold: 0.568 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	11 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.559 TurboFold(seed): 0.544 Sensitivity PknotsRG: 0.491 TurboFold(seed): 0.439 Positive Predictive Value PknotsRG: 0.643 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.151222316e-07	11 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.544 ProbKnot: 0.499 Sensitivity TurboFold(seed): 0.439 ProbKnot: 0.437 Positive Predictive Value TurboFold(seed): 0.679 ProbKnot: 0.577 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	9 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Murlet(20): 0.521 Sensitivity TurboFold(seed): 0.454 Murlet(20): 0.384 Positive Predictive Value TurboFold(seed): 0.708 Murlet(20): 0.712 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAfold: 0.525 Sensitivity TurboFold(seed): 0.439 RNAfold: 0.456 Positive Predictive Value TurboFold(seed): 0.679 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.89857672583e-08	9 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Carnac(20): 0.493 Sensitivity TurboFold(seed): 0.454 Carnac(20): 0.286 Positive Predictive Value TurboFold(seed): 0.708 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAshapes: 0.520 Sensitivity TurboFold(seed): 0.439 RNAshapes: 0.453 Positive Predictive Value TurboFold(seed): 0.679 RNAshapes: 0.604 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.92661845584e-08	11 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.544 Fold: 0.447 Sensitivity TurboFold(seed): 0.439 Fold: 0.394 Positive Predictive Value TurboFold(seed): 0.679 Fold: 0.516 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08		+ TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.510 RSpredict(20): 0.404 Sensitivity TurboFold(seed): 0.419 RSpredict(20): 0.313 Positive Predictive Value TurboFold(seed): 0.626 RSpredict(20): 0.529 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.571 TurboFold(seed): 0.470 Sensitivity Afold: 0.524 TurboFold(seed): 0.413 Positive Predictive Value Afold: 0.629 TurboFold(seed): 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAsubopt: 0.488 Sensitivity TurboFold(seed): 0.439 RNAsubopt: 0.426 Positive Predictive Value TurboFold(seed): 0.679 RNAsubopt: 0.566 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	? TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.478 RNASLOpt: 0.395 Sensitivity TurboFold(seed): 0.382 RNASLOpt: 0.320 Positive Predictive Value TurboFold(seed): 0.603 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.620 TurboFold(seed): 0.613 Sensitivity Cylofold: 0.504 TurboFold(seed): 0.487 Positive Predictive Value Cylofold: 0.770 TurboFold(seed): 0.779 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.544 McQFold: 0.527 Sensitivity TurboFold(seed): 0.439 McQFold: 0.450 Positive Predictive Value TurboFold(seed): 0.679 McQFold: 0.623 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000799494419018	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Multilign(20): 0.568 Sensitivity TurboFold(seed): 0.490 Multilign(20): 0.483 Positive Predictive Value TurboFold(seed): 0.729 Multilign(20): 0.676 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 TurboFold(seed): 0.483 Sensitivity CRWrnafold: 0.428 TurboFold(seed): 0.397 Positive Predictive Value CRWrnafold: 0.554 TurboFold(seed): 0.595 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.544 Pknots: 0.450 Sensitivity TurboFold(seed): 0.439 Pknots: 0.407 Positive Predictive Value TurboFold(seed): 0.679 Pknots: 0.505 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.461 TurboFold(seed): 0.458 Sensitivity RNASampler(seed): 0.323 TurboFold(seed): 0.383 Positive Predictive Value RNASampler(seed): 0.663 TurboFold(seed): 0.554 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.624 TurboFold(seed): 0.594 Sensitivity Alterna: 0.534 TurboFold(seed): 0.500 Positive Predictive Value Alterna: 0.738 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Mastr(20): 0.523 Sensitivity TurboFold(seed): 0.454 Mastr(20): 0.333 Positive Predictive Value TurboFold(seed): 0.708 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.550 Vsfold4: 0.423 Sensitivity TurboFold(seed): 0.456 Vsfold4: 0.346 Positive Predictive Value TurboFold(seed): 0.672 Vsfold4: 0.527 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.518 Murlet(seed): 0.464 Sensitivity TurboFold(seed): 0.416 Murlet(seed): 0.268 Positive Predictive Value TurboFold(seed): 0.650 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.35568223474e-09	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.566 Vsfold5: 0.380 Sensitivity TurboFold(seed): 0.467 Vsfold5: 0.326 Positive Predictive Value TurboFold(seed): 0.693 Vsfold5: 0.452 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.515 MCFold: 0.383 Sensitivity TurboFold(seed): 0.427 MCFold: 0.396 Positive Predictive Value TurboFold(seed): 0.627 MCFold: 0.377 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.598 RDfolder: 0.467 Sensitivity TurboFold(seed): 0.474 RDfolder: 0.352 Positive Predictive Value TurboFold(seed): 0.762 RDfolder: 0.633 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAwolf: 0.297 Sensitivity TurboFold(seed): 0.434 RNAwolf: 0.282 Positive Predictive Value TurboFold(seed): 0.650 RNAwolf: 0.321 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.13260312532e-08	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.439 NanoFolder: 0.341 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.351 Positive Predictive Value TurboFold(seed): 0.530 NanoFolder: 0.339 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.563 Multilign(seed): 0.507 Sensitivity TurboFold(seed): 0.443 Multilign(seed): 0.386 Positive Predictive Value TurboFold(seed): 0.722 Multilign(seed): 0.674 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.518 PPfold(seed): 0.127 Sensitivity TurboFold(seed): 0.413 PPfold(seed): 0.031 Positive Predictive Value TurboFold(seed): 0.656 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.33795641379e-09	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.547 RSpredict(seed): 0.236 Sensitivity TurboFold(seed): 0.452 RSpredict(seed): 0.108 Positive Predictive Value TurboFold(seed): 0.667 RSpredict(seed): 0.524 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.544 Carnac(seed): 0.248 Sensitivity TurboFold(seed): 0.439 Carnac(seed): 0.062 Positive Predictive Value TurboFold(seed): 0.679 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.544 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.439 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.679 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.02533530638e-08	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity TurboFold(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RSpredict(20)	38 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RSpredict(20): 0.541 Sensitivity CentroidAlifold(20): 0.518 RSpredict(20): 0.422 Positive Predictive Value CentroidAlifold(20): 0.877 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.669 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.534 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(seed): 0.841 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	17 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.605 RSpredict(20): 0.491 Sensitivity ContextFold: 0.492 RSpredict(20): 0.373 Positive Predictive Value ContextFold: 0.749 RSpredict(20): 0.653 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	38 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.648 RSpredict(20): 0.539 Sensitivity MXScarna(seed): 0.534 RSpredict(20): 0.420 Positive Predictive Value MXScarna(seed): 0.789 RSpredict(20): 0.697 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.645 RSpredict(20): 0.544 Sensitivity RNAalifold(20): 0.499 RSpredict(20): 0.425 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	21 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.662 RSpredict(20): 0.521 Sensitivity PPfold(20): 0.526 RSpredict(20): 0.401 Positive Predictive Value PPfold(20): 0.837 RSpredict(20): 0.683 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	20 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.535 RSpredict(20): 0.520 Sensitivity IPknot: 0.443 RSpredict(20): 0.398 Positive Predictive Value IPknot: 0.651 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.18891756672e-06	38 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RSpredict(20): 0.541 Sensitivity CentroidAlifold(seed): 0.383 RSpredict(20): 0.422 Positive Predictive Value CentroidAlifold(seed): 0.922 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.612 RSpredict(20): 0.544 Sensitivity RNASampler(20): 0.471 RSpredict(20): 0.425 Positive Predictive Value RNASampler(20): 0.798 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.625 RSpredict(20): 0.521 Sensitivity TurboFold(20): 0.518 RSpredict(20): 0.401 Positive Predictive Value TurboFold(20): 0.759 RSpredict(20): 0.683 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	39 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.615 RSpredict(20): 0.544 Sensitivity MXScarna(20): 0.514 RSpredict(20): 0.425 Positive Predictive Value MXScarna(20): 0.740 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.563 RSpredict(20): 0.544 Sensitivity Sfold: 0.476 RSpredict(20): 0.425 Positive Predictive Value Sfold: 0.671 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.62644058675e-08	20 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 RSpredict(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.512 RSpredict(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.708 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	39 RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.544 Contrafold: 0.539 Sensitivity RSpredict(20): 0.425 Contrafold: 0.480 Positive Predictive Value RSpredict(20): 0.701 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000332169954379	22 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.556 RSpredict(20): 0.435 Sensitivity RNAalifold(seed): 0.333 RSpredict(20): 0.328 Positive Predictive Value RNAalifold(seed): 0.932 RSpredict(20): 0.583 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	39 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.544 HotKnots: 0.535 Sensitivity RSpredict(20): 0.425 HotKnots: 0.482 Positive Predictive Value RSpredict(20): 0.701 HotKnots: 0.600 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000150377120024	38 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.555 RSpredict(20): 0.541 Sensitivity MaxExpect: 0.483 RSpredict(20): 0.422 Positive Predictive Value MaxExpect: 0.641 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.541 CentroidFold: 0.540 Sensitivity RSpredict(20): 0.422 CentroidFold: 0.459 Positive Predictive Value RSpredict(20): 0.699 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.777738600652	39 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.545 RSpredict(20): 0.544 Sensitivity UNAFold: 0.482 RSpredict(20): 0.425 Positive Predictive Value UNAFold: 0.620 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.736846409308	39 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.558 RSpredict(20): 0.544 Sensitivity PknotsRG: 0.500 RSpredict(20): 0.425 Positive Predictive Value PknotsRG: 0.627 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 4.59499054376e-07	30 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.546 RSpredict(20): 0.529 Sensitivity ProbKnot: 0.486 RSpredict(20): 0.409 Positive Predictive Value ProbKnot: 0.617 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.48494289621e-08	39 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.581 RSpredict(20): 0.544 Sensitivity Murlet(20): 0.431 RSpredict(20): 0.425 Positive Predictive Value Murlet(20): 0.789 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.544 RNAfold: 0.542 Sensitivity RSpredict(20): 0.425 RNAfold: 0.484 Positive Predictive Value RSpredict(20): 0.701 RNAfold: 0.610 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.150371979191	39 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.580 RSpredict(20): 0.544 Sensitivity Carnac(20): 0.376 RSpredict(20): 0.425 Positive Predictive Value Carnac(20): 0.898 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.551 RSpredict(20): 0.544 Sensitivity RNAshapes: 0.488 RSpredict(20): 0.425 Positive Predictive Value RNAshapes: 0.625 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 7.75845522374e-05	30 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.553 RSpredict(20): 0.529 Sensitivity Fold: 0.495 RSpredict(20): 0.409 Positive Predictive Value Fold: 0.624 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.18450348589e-07	11 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.510 RSpredict(20): 0.404 Sensitivity TurboFold(seed): 0.419 RSpredict(20): 0.313 Positive Predictive Value TurboFold(seed): 0.626 RSpredict(20): 0.529 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08		+ RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.543 Afold: 0.518 Sensitivity RSpredict(20): 0.449 Afold: 0.473 Positive Predictive Value RSpredict(20): 0.660 Afold: 0.571 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.27821480483e-07	= RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.548 RSpredict(20): 0.544 Sensitivity RNAsubopt: 0.494 RSpredict(20): 0.425 Positive Predictive Value RNAsubopt: 0.612 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00107053140167	+ RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.491 RNASLOpt: 0.464 Sensitivity RSpredict(20): 0.373 RNASLOpt: 0.387 Positive Predictive Value RSpredict(20): 0.653 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.87745389242e-07	- Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.608 RSpredict(20): 0.589 Sensitivity Cylofold: 0.524 RSpredict(20): 0.451 Positive Predictive Value Cylofold: 0.711 RSpredict(20): 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.61189297362e-07	+ RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.544 McQFold: 0.513 Sensitivity RSpredict(20): 0.425 McQFold: 0.445 Positive Predictive Value RSpredict(20): 0.701 McQFold: 0.597 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.535 Multilign(20): 0.526 Sensitivity RSpredict(20): 0.405 Multilign(20): 0.437 Positive Predictive Value RSpredict(20): 0.712 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.000406393755088	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.546 RSpredict(20): 0.446 Sensitivity CRWrnafold: 0.483 RSpredict(20): 0.331 Positive Predictive Value CRWrnafold: 0.623 RSpredict(20): 0.609 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.545 Pknots: 0.490 Sensitivity RSpredict(20): 0.424 Pknots: 0.447 Positive Predictive Value RSpredict(20): 0.707 Pknots: 0.544 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.492 RSpredict(20): 0.423 Sensitivity RNASampler(seed): 0.364 RSpredict(20): 0.369 Positive Predictive Value RNASampler(seed): 0.668 RSpredict(20): 0.489 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.29018360962e-08	+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.667 Alterna: 0.571 Sensitivity RSpredict(20): 0.526 Alterna: 0.504 Positive Predictive Value RSpredict(20): 0.853 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.544 Mastr(20): 0.515 Sensitivity RSpredict(20): 0.425 Mastr(20): 0.345 Positive Predictive Value RSpredict(20): 0.701 Mastr(20): 0.773 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.554 Vsfold4: 0.459 Sensitivity RSpredict(20): 0.433 Vsfold4: 0.387 Positive Predictive Value RSpredict(20): 0.713 Vsfold4: 0.549 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.454 RSpredict(20): 0.416 Sensitivity Murlet(seed): 0.238 RSpredict(20): 0.309 Positive Predictive Value Murlet(seed): 0.869 RSpredict(20): 0.569 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.554 Vsfold5: 0.417 Sensitivity RSpredict(20): 0.433 Vsfold5: 0.358 Positive Predictive Value RSpredict(20): 0.713 Vsfold5: 0.493 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.563 MCFold: 0.401 Sensitivity RSpredict(20): 0.448 MCFold: 0.418 Positive Predictive Value RSpredict(20): 0.712 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.642 RDfolder: 0.551 Sensitivity RSpredict(20): 0.493 RDfolder: 0.449 Positive Predictive Value RSpredict(20): 0.843 RDfolder: 0.686 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.520 RNAwolf: 0.343 Sensitivity RSpredict(20): 0.398 RNAwolf: 0.325 Positive Predictive Value RSpredict(20): 0.685 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.566 CMfinder(20): 0.539 Sensitivity RSpredict(20): 0.443 CMfinder(20): 0.389 Positive Predictive Value RSpredict(20): 0.729 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.511 NanoFolder: 0.271 Sensitivity RSpredict(20): 0.394 NanoFolder: 0.286 Positive Predictive Value RSpredict(20): 0.667 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.58287649515e-08	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.542 RSpredict(20): 0.423 Sensitivity Multilign(seed): 0.413 RSpredict(20): 0.323 Positive Predictive Value Multilign(seed): 0.719 RSpredict(20): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.520 PPfold(seed): 0.072 Sensitivity RSpredict(20): 0.398 PPfold(seed): 0.012 Positive Predictive Value RSpredict(20): 0.685 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.535 RSpredict(seed): 0.280 Sensitivity RSpredict(20): 0.408 RSpredict(seed): 0.133 Positive Predictive Value RSpredict(20): 0.703 RSpredict(seed): 0.594 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.466 Carnac(seed): 0.179 Sensitivity RSpredict(20): 0.355 Carnac(seed): 0.032 Positive Predictive Value RSpredict(20): 0.618 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.544 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.425 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.701 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Afold	19 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.635 Afold: 0.511 Sensitivity CentroidAlifold(20): 0.476 Afold: 0.467 Positive Predictive Value CentroidAlifold(20): 0.850 Afold: 0.564 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	6 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.639 Afold: 0.453 Sensitivity PETfold_pre2.0(seed): 0.521 Afold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Afold: 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	28 Afold vs ContextFold Matthews Correlation Coefficient Afold: 0.426 ContextFold: 0.424 Sensitivity Afold: 0.385 ContextFold: 0.355 Positive Predictive Value Afold: 0.473 ContextFold: 0.509 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00757664188007	34 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.669 Afold: 0.574 Sensitivity MXScarna(seed): 0.562 Afold: 0.534 Positive Predictive Value MXScarna(seed): 0.800 Afold: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.611 Afold: 0.530 Sensitivity RNAalifold(20): 0.466 Afold: 0.478 Positive Predictive Value RNAalifold(20): 0.804 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	4 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.526 Afold: 0.416 Sensitivity PETfold_pre2.0(20): 0.410 Afold: 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.679 Afold: 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.623 Afold: 0.611 Sensitivity PPfold(20): 0.484 Afold: 0.548 Positive Predictive Value PPfold(20): 0.806 Afold: 0.685 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	34 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.494 Afold: 0.443 Sensitivity IPknot: 0.388 Afold: 0.400 Positive Predictive Value IPknot: 0.630 Afold: 0.492 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.599 Afold: 0.559 Sensitivity CentroidAlifold(seed): 0.418 Afold: 0.520 Positive Predictive Value CentroidAlifold(seed): 0.861 Afold: 0.605 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.602 Afold: 0.530 Sensitivity RNASampler(20): 0.455 Afold: 0.478 Positive Predictive Value RNASampler(20): 0.801 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	5 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.646 Afold: 0.611 Sensitivity TurboFold(20): 0.535 Afold: 0.548 Positive Predictive Value TurboFold(20): 0.783 Afold: 0.685 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	20 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.607 Afold: 0.530 Sensitivity MXScarna(20): 0.514 Afold: 0.478 Positive Predictive Value MXScarna(20): 0.721 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.492 Afold: 0.468 Sensitivity Sfold: 0.419 Afold: 0.425 Positive Predictive Value Sfold: 0.577 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.595 Afold: 0.585 Sensitivity CentroidHomfold‑LAST: 0.454 Afold: 0.527 Positive Predictive Value CentroidHomfold‑LAST: 0.786 Afold: 0.655 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.00842627253913	105 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.534 Afold: 0.468 Sensitivity Contrafold: 0.473 Afold: 0.425 Positive Predictive Value Contrafold: 0.603 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.602 RNAalifold(seed): 0.576 Sensitivity Afold: 0.565 RNAalifold(seed): 0.383 Positive Predictive Value Afold: 0.646 RNAalifold(seed): 0.867 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	101 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.639 Afold: 0.615 Sensitivity HotKnots: 0.583 Afold: 0.563 Positive Predictive Value HotKnots: 0.705 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	83 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.555 Afold: 0.511 Sensitivity MaxExpect: 0.487 Afold: 0.458 Positive Predictive Value MaxExpect: 0.633 Afold: 0.571 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	94 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.524 Afold: 0.469 Sensitivity CentroidFold: 0.439 Afold: 0.431 Positive Predictive Value CentroidFold: 0.625 Afold: 0.510 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.474 Afold: 0.468 Sensitivity UNAFold: 0.425 Afold: 0.425 Positive Predictive Value UNAFold: 0.529 Afold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.468 PknotsRG: 0.460 Sensitivity Afold: 0.425 PknotsRG: 0.417 Positive Predictive Value Afold: 0.517 PknotsRG: 0.507 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.535 Afold: 0.521 Sensitivity ProbKnot: 0.491 Afold: 0.479 Positive Predictive Value ProbKnot: 0.584 Afold: 0.568 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	20 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.558 Afold: 0.530 Sensitivity Murlet(20): 0.408 Afold: 0.478 Positive Predictive Value Murlet(20): 0.766 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.15842348871e-07	105 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.468 RNAfold: 0.468 Sensitivity Afold: 0.425 RNAfold: 0.424 Positive Predictive Value Afold: 0.517 RNAfold: 0.517 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.360712528037	20 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.587 Afold: 0.530 Sensitivity Carnac(20): 0.372 Afold: 0.478 Positive Predictive Value Carnac(20): 0.929 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	101 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.622 Afold: 0.615 Sensitivity RNAshapes: 0.561 Afold: 0.563 Positive Predictive Value RNAshapes: 0.694 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.39704516867e-06	67 Fold vs Afold Matthews Correlation Coefficient Fold: 0.560 Afold: 0.546 Sensitivity Fold: 0.514 Afold: 0.502 Positive Predictive Value Fold: 0.612 Afold: 0.594 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.85233844192e-08	5 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.571 TurboFold(seed): 0.470 Sensitivity Afold: 0.524 TurboFold(seed): 0.413 Positive Predictive Value Afold: 0.629 TurboFold(seed): 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	20 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.543 Afold: 0.518 Sensitivity RSpredict(20): 0.449 Afold: 0.473 Positive Predictive Value RSpredict(20): 0.660 Afold: 0.571 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.27821480483e-07		- RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.620 Afold: 0.615 Sensitivity RNAsubopt: 0.566 Afold: 0.563 Positive Predictive Value RNAsubopt: 0.685 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.49438993542e-06	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.540 RNASLOpt: 0.535 Sensitivity Afold: 0.489 RNASLOpt: 0.460 Positive Predictive Value Afold: 0.603 RNASLOpt: 0.629 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000138311429829	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.658 Cylofold: 0.611 Sensitivity Afold: 0.597 Cylofold: 0.525 Positive Predictive Value Afold: 0.731 Cylofold: 0.717 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.467 McQFold: 0.391 Sensitivity Afold: 0.423 McQFold: 0.309 Positive Predictive Value Afold: 0.516 McQFold: 0.495 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.555 Multilign(20): 0.500 Sensitivity Afold: 0.497 Multilign(20): 0.416 Positive Predictive Value Afold: 0.624 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.638 CRWrnafold: 0.564 Sensitivity Afold: 0.592 CRWrnafold: 0.515 Positive Predictive Value Afold: 0.695 CRWrnafold: 0.627 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ Afold vs Pknots Matthews Correlation Coefficient Afold: 0.662 Pknots: 0.639 Sensitivity Afold: 0.602 Pknots: 0.587 Positive Predictive Value Afold: 0.733 Pknots: 0.702 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.695 RNASampler(seed): 0.669 Sensitivity Afold: 0.649 RNASampler(seed): 0.528 Positive Predictive Value Afold: 0.749 RNASampler(seed): 0.852 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.710 Alterna: 0.683 Sensitivity Afold: 0.647 Alterna: 0.618 Positive Predictive Value Afold: 0.788 Alterna: 0.763 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.544 Afold: 0.530 Sensitivity Mastr(20): 0.367 Afold: 0.478 Positive Predictive Value Mastr(20): 0.811 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.4733335145e-06	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.625 Vsfold4: 0.553 Sensitivity Afold: 0.571 Vsfold4: 0.474 Positive Predictive Value Afold: 0.689 Vsfold4: 0.652 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.677 Murlet(seed): 0.545 Sensitivity Afold: 0.617 Murlet(seed): 0.357 Positive Predictive Value Afold: 0.747 Murlet(seed): 0.837 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.623 Vsfold5: 0.518 Sensitivity Afold: 0.569 Vsfold5: 0.450 Positive Predictive Value Afold: 0.687 Vsfold5: 0.602 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.660 MCFold: 0.578 Sensitivity Afold: 0.605 MCFold: 0.599 Positive Predictive Value Afold: 0.727 MCFold: 0.565 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.704 RDfolder: 0.621 Sensitivity Afold: 0.641 RDfolder: 0.522 Positive Predictive Value Afold: 0.781 RDfolder: 0.748 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.439 RNAwolf: 0.318 Sensitivity Afold: 0.397 RNAwolf: 0.298 Positive Predictive Value Afold: 0.488 RNAwolf: 0.342 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.723 CMfinder(20): 0.577 Sensitivity Afold: 0.612 CMfinder(20): 0.388 Positive Predictive Value Afold: 0.857 CMfinder(20): 0.864 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.546 NanoFolder: 0.386 Sensitivity Afold: 0.495 NanoFolder: 0.406 Positive Predictive Value Afold: 0.607 NanoFolder: 0.374 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.693 Afold: 0.680 Sensitivity Multilign(seed): 0.579 Afold: 0.596 Positive Predictive Value Multilign(seed): 0.835 Afold: 0.782 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.547 PPfold(seed): 0.138 Sensitivity Afold: 0.487 PPfold(seed): 0.036 Positive Predictive Value Afold: 0.621 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.563 RSpredict(seed): 0.361 Sensitivity Afold: 0.524 RSpredict(seed): 0.197 Positive Predictive Value Afold: 0.609 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.668 Carnac(seed): 0.302 Sensitivity Afold: 0.614 Carnac(seed): 0.092 Positive Predictive Value Afold: 0.732 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.570 Mastr(seed): 0.293 Sensitivity Afold: 0.526 Mastr(seed): 0.096 Positive Predictive Value Afold: 0.621 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAsubopt	39 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RNAsubopt: 0.544 Sensitivity CentroidAlifold(20): 0.516 RNAsubopt: 0.488 Positive Predictive Value CentroidAlifold(20): 0.879 RNAsubopt: 0.611 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAsubopt: 0.525 Sensitivity PETfold_pre2.0(seed): 0.595 RNAsubopt: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	47 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.633 RNAsubopt: 0.511 Sensitivity ContextFold: 0.523 RNAsubopt: 0.452 Positive Predictive Value ContextFold: 0.769 RNAsubopt: 0.582 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.666 RNAsubopt: 0.572 Sensitivity MXScarna(seed): 0.554 RNAsubopt: 0.520 Positive Predictive Value MXScarna(seed): 0.804 RNAsubopt: 0.633 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAsubopt: 0.549 Sensitivity RNAalifold(20): 0.502 RNAsubopt: 0.490 Positive Predictive Value RNAalifold(20): 0.860 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAsubopt: 0.505 Sensitivity PETfold_pre2.0(20): 0.530 RNAsubopt: 0.451 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	15 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.691 RNAsubopt: 0.565 Sensitivity PPfold(20): 0.544 RNAsubopt: 0.495 Positive Predictive Value PPfold(20): 0.881 RNAsubopt: 0.652 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	55 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.615 RNAsubopt: 0.528 Sensitivity IPknot: 0.512 RNAsubopt: 0.466 Positive Predictive Value IPknot: 0.742 RNAsubopt: 0.603 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 RNAsubopt: 0.565 Sensitivity CentroidAlifold(seed): 0.397 RNAsubopt: 0.513 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.623 RNAsubopt: 0.549 Sensitivity RNASampler(20): 0.470 RNAsubopt: 0.490 Positive Predictive Value RNASampler(20): 0.830 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.655 RNAsubopt: 0.565 Sensitivity TurboFold(20): 0.529 RNAsubopt: 0.495 Positive Predictive Value TurboFold(20): 0.816 RNAsubopt: 0.652 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	34 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.624 RNAsubopt: 0.549 Sensitivity MXScarna(20): 0.518 RNAsubopt: 0.490 Positive Predictive Value MXScarna(20): 0.756 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.640 RNAsubopt: 0.595 Sensitivity Sfold: 0.548 RNAsubopt: 0.534 Positive Predictive Value Sfold: 0.751 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 RNAsubopt: 0.561 Sensitivity CentroidHomfold‑LAST: 0.439 RNAsubopt: 0.493 Positive Predictive Value CentroidHomfold‑LAST: 0.789 RNAsubopt: 0.642 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.618 RNAsubopt: 0.595 Sensitivity Contrafold: 0.550 RNAsubopt: 0.534 Positive Predictive Value Contrafold: 0.700 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.596 RNAsubopt: 0.569 Sensitivity RNAalifold(seed): 0.397 RNAsubopt: 0.521 Positive Predictive Value RNAalifold(seed): 0.897 RNAsubopt: 0.625 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.622 RNAsubopt: 0.595 Sensitivity HotKnots: 0.558 RNAsubopt: 0.534 Positive Predictive Value HotKnots: 0.699 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	115 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.610 RNAsubopt: 0.595 Sensitivity MaxExpect: 0.539 RNAsubopt: 0.536 Positive Predictive Value MaxExpect: 0.695 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	133 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.601 RNAsubopt: 0.590 Sensitivity CentroidFold: 0.515 RNAsubopt: 0.531 Positive Predictive Value CentroidFold: 0.706 RNAsubopt: 0.659 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.48494289621e-08	135 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.624 RNAsubopt: 0.595 Sensitivity UNAFold: 0.554 RNAsubopt: 0.534 Positive Predictive Value UNAFold: 0.707 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.608 RNAsubopt: 0.595 Sensitivity PknotsRG: 0.544 RNAsubopt: 0.534 Positive Predictive Value PknotsRG: 0.683 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.594 RNAsubopt: 0.588 Sensitivity ProbKnot: 0.537 RNAsubopt: 0.530 Positive Predictive Value ProbKnot: 0.661 RNAsubopt: 0.657 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 1.83595875043e-07	34 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.577 RNAsubopt: 0.549 Sensitivity Murlet(20): 0.423 RNAsubopt: 0.490 Positive Predictive Value Murlet(20): 0.791 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.613 RNAsubopt: 0.595 Sensitivity RNAfold: 0.547 RNAsubopt: 0.534 Positive Predictive Value RNAfold: 0.691 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.577 RNAsubopt: 0.549 Sensitivity Carnac(20): 0.372 RNAsubopt: 0.490 Positive Predictive Value Carnac(20): 0.897 RNAsubopt: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.602 RNAsubopt: 0.595 Sensitivity RNAshapes: 0.533 RNAsubopt: 0.534 Positive Predictive Value RNAshapes: 0.685 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 1.97386617324e-07	99 RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.605 Fold: 0.605 Sensitivity RNAsubopt: 0.546 Fold: 0.544 Positive Predictive Value RNAsubopt: 0.675 Fold: 0.676 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.264581540075	11 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.544 RNAsubopt: 0.488 Sensitivity TurboFold(seed): 0.439 RNAsubopt: 0.426 Positive Predictive Value TurboFold(seed): 0.679 RNAsubopt: 0.566 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	39 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.548 RSpredict(20): 0.544 Sensitivity RNAsubopt: 0.494 RSpredict(20): 0.425 Positive Predictive Value RNAsubopt: 0.612 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00107053140167	101 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.620 Afold: 0.615 Sensitivity RNAsubopt: 0.566 Afold: 0.563 Positive Predictive Value RNAsubopt: 0.685 Afold: 0.677 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.49438993542e-06		+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.511 RNASLOpt: 0.489 Sensitivity RNAsubopt: 0.452 RNASLOpt: 0.393 Positive Predictive Value RNAsubopt: 0.582 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.647 Cylofold: 0.607 Sensitivity RNAsubopt: 0.576 Cylofold: 0.517 Positive Predictive Value RNAsubopt: 0.733 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.594 McQFold: 0.571 Sensitivity RNAsubopt: 0.533 McQFold: 0.492 Positive Predictive Value RNAsubopt: 0.666 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.590 Multilign(20): 0.561 Sensitivity RNAsubopt: 0.518 Multilign(20): 0.466 Positive Predictive Value RNAsubopt: 0.678 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	- CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.585 RNAsubopt: 0.583 Sensitivity CRWrnafold: 0.522 RNAsubopt: 0.524 Positive Predictive Value CRWrnafold: 0.663 RNAsubopt: 0.656 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.19883461079e-06	+ RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.634 Pknots: 0.601 Sensitivity RNAsubopt: 0.568 Pknots: 0.545 Positive Predictive Value RNAsubopt: 0.713 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.635 RNAsubopt: 0.616 Sensitivity RNASampler(seed): 0.484 RNAsubopt: 0.571 Positive Predictive Value RNASampler(seed): 0.837 RNAsubopt: 0.670 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.41690547646e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.692 Alterna: 0.665 Sensitivity RNAsubopt: 0.616 Alterna: 0.599 Positive Predictive Value RNAsubopt: 0.786 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.549 Mastr(20): 0.514 Sensitivity RNAsubopt: 0.490 Mastr(20): 0.339 Positive Predictive Value RNAsubopt: 0.620 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.618 Vsfold4: 0.547 Sensitivity RNAsubopt: 0.557 Vsfold4: 0.465 Positive Predictive Value RNAsubopt: 0.691 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.600 Murlet(seed): 0.514 Sensitivity RNAsubopt: 0.538 Murlet(seed): 0.315 Positive Predictive Value RNAsubopt: 0.674 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.619 Vsfold5: 0.510 Sensitivity RNAsubopt: 0.557 Vsfold5: 0.441 Positive Predictive Value RNAsubopt: 0.693 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.625 MCFold: 0.522 Sensitivity RNAsubopt: 0.564 MCFold: 0.535 Positive Predictive Value RNAsubopt: 0.698 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.689 RDfolder: 0.592 Sensitivity RNAsubopt: 0.614 RDfolder: 0.491 Positive Predictive Value RNAsubopt: 0.781 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.532 RNAwolf: 0.385 Sensitivity RNAsubopt: 0.471 RNAwolf: 0.360 Positive Predictive Value RNAsubopt: 0.606 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.577 CMfinder(20): 0.546 Sensitivity RNAsubopt: 0.506 CMfinder(20): 0.366 Positive Predictive Value RNAsubopt: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.553 NanoFolder: 0.339 Sensitivity RNAsubopt: 0.493 NanoFolder: 0.350 Positive Predictive Value RNAsubopt: 0.627 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.558 RNAsubopt: 0.555 Sensitivity Multilign(seed): 0.434 RNAsubopt: 0.476 Positive Predictive Value Multilign(seed): 0.725 RNAsubopt: 0.654 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.539 PPfold(seed): 0.092 Sensitivity RNAsubopt: 0.469 PPfold(seed): 0.016 Positive Predictive Value RNAsubopt: 0.626 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.568 RSpredict(seed): 0.266 Sensitivity RNAsubopt: 0.517 RSpredict(seed): 0.128 Positive Predictive Value RNAsubopt: 0.628 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.614 Carnac(seed): 0.241 Sensitivity RNAsubopt: 0.553 Carnac(seed): 0.058 Positive Predictive Value RNAsubopt: 0.686 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.564 Mastr(seed): 0.236 Sensitivity RNAsubopt: 0.511 Mastr(seed): 0.062 Positive Predictive Value RNAsubopt: 0.626 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAsubopt: 0.685 Sensitivity PETfold_2.0(seed): 0.642 RNAsubopt: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAsubopt: 0.831 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAsubopt: 0.542 Sensitivity PETfold_2.0(20): 0.509 RNAsubopt: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASLOpt	18 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.656 RNASLOpt: 0.463 Sensitivity CentroidAlifold(20): 0.501 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.864 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	25 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNASLOpt: 0.499 Sensitivity PETfold_pre2.0(seed): 0.595 RNASLOpt: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	47 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.633 RNASLOpt: 0.489 Sensitivity ContextFold: 0.523 RNASLOpt: 0.393 Positive Predictive Value ContextFold: 0.769 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.611 RNASLOpt: 0.533 Sensitivity MXScarna(seed): 0.489 RNASLOpt: 0.431 Positive Predictive Value MXScarna(seed): 0.770 RNASLOpt: 0.666 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	11 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.645 RNASLOpt: 0.540 Sensitivity RNAalifold(20): 0.493 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(20): 0.847 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	18 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASLOpt: 0.463 Sensitivity PETfold_pre2.0(20): 0.530 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	11 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.680 RNASLOpt: 0.540 Sensitivity PPfold(20): 0.537 RNASLOpt: 0.443 Positive Predictive Value PPfold(20): 0.865 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.53487163866e-09	47 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.604 RNASLOpt: 0.489 Sensitivity IPknot: 0.503 RNASLOpt: 0.393 Positive Predictive Value IPknot: 0.728 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.558 RNASLOpt: 0.499 Sensitivity CentroidAlifold(seed): 0.334 RNASLOpt: 0.408 Positive Predictive Value CentroidAlifold(seed): 0.936 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.575 RNASLOpt: 0.540 Sensitivity RNASampler(20): 0.431 RNASLOpt: 0.443 Positive Predictive Value RNASampler(20): 0.771 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.79203144115e-08	11 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.635 RNASLOpt: 0.540 Sensitivity TurboFold(20): 0.507 RNASLOpt: 0.443 Positive Predictive Value TurboFold(20): 0.798 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	11 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.564 RNASLOpt: 0.540 Sensitivity MXScarna(20): 0.456 RNASLOpt: 0.443 Positive Predictive Value MXScarna(20): 0.703 RNASLOpt: 0.664 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.79393067223e-08	47 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.575 RNASLOpt: 0.489 Sensitivity Sfold: 0.478 RNASLOpt: 0.393 Positive Predictive Value Sfold: 0.696 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.559 RNASLOpt: 0.512 Sensitivity CentroidHomfold‑LAST: 0.417 RNASLOpt: 0.409 Positive Predictive Value CentroidHomfold‑LAST: 0.753 RNASLOpt: 0.646 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.548 RNASLOpt: 0.489 Sensitivity Contrafold: 0.474 RNASLOpt: 0.393 Positive Predictive Value Contrafold: 0.637 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.552 RNASLOpt: 0.426 Sensitivity RNAalifold(seed): 0.348 RNASLOpt: 0.352 Positive Predictive Value RNAalifold(seed): 0.879 RNASLOpt: 0.523 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	47 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.549 RNASLOpt: 0.489 Sensitivity HotKnots: 0.485 RNASLOpt: 0.393 Positive Predictive Value HotKnots: 0.626 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.531 RNASLOpt: 0.489 Sensitivity MaxExpect: 0.454 RNASLOpt: 0.393 Positive Predictive Value MaxExpect: 0.626 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.508 RNASLOpt: 0.488 Sensitivity CentroidFold: 0.422 RNASLOpt: 0.395 Positive Predictive Value CentroidFold: 0.617 RNASLOpt: 0.607 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.532 RNASLOpt: 0.489 Sensitivity UNAFold: 0.466 RNASLOpt: 0.393 Positive Predictive Value UNAFold: 0.611 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.543 RNASLOpt: 0.489 Sensitivity PknotsRG: 0.477 RNASLOpt: 0.393 Positive Predictive Value PknotsRG: 0.622 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.530 RNASLOpt: 0.489 Sensitivity ProbKnot: 0.467 RNASLOpt: 0.393 Positive Predictive Value ProbKnot: 0.607 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Murlet(20): 0.532 Sensitivity RNASLOpt: 0.443 Murlet(20): 0.394 Positive Predictive Value RNASLOpt: 0.664 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0291093487101	47 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.541 RNASLOpt: 0.489 Sensitivity RNAfold: 0.472 RNASLOpt: 0.393 Positive Predictive Value RNAfold: 0.624 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Carnac(20): 0.524 Sensitivity RNASLOpt: 0.443 Carnac(20): 0.337 Positive Predictive Value RNASLOpt: 0.664 Carnac(20): 0.820 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.81657399344e-06	47 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.512 RNASLOpt: 0.489 Sensitivity RNAshapes: 0.447 RNASLOpt: 0.393 Positive Predictive Value RNAshapes: 0.593 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.496 RNASLOpt: 0.489 Sensitivity Fold: 0.438 RNASLOpt: 0.393 Positive Predictive Value Fold: 0.567 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 2.29562105844e-05	8 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.478 RNASLOpt: 0.395 Sensitivity TurboFold(seed): 0.382 RNASLOpt: 0.320 Positive Predictive Value TurboFold(seed): 0.603 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.491 RNASLOpt: 0.464 Sensitivity RSpredict(20): 0.373 RNASLOpt: 0.387 Positive Predictive Value RSpredict(20): 0.653 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.87745389242e-07	27 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.540 RNASLOpt: 0.535 Sensitivity Afold: 0.489 RNASLOpt: 0.460 Positive Predictive Value Afold: 0.603 RNASLOpt: 0.629 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000138311429829	47 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.511 RNASLOpt: 0.489 Sensitivity RNAsubopt: 0.452 RNASLOpt: 0.393 Positive Predictive Value RNAsubopt: 0.582 RNASLOpt: 0.614 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.539 Cylofold: 0.522 Sensitivity RNASLOpt: 0.445 Cylofold: 0.436 Positive Predictive Value RNASLOpt: 0.658 Cylofold: 0.632 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.483 McQFold: 0.474 Sensitivity RNASLOpt: 0.387 McQFold: 0.401 Positive Predictive Value RNASLOpt: 0.608 McQFold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 9.69999390915e-05	+ RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.580 Multilign(20): 0.557 Sensitivity RNASLOpt: 0.477 Multilign(20): 0.472 Positive Predictive Value RNASLOpt: 0.710 Multilign(20): 0.663 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.76965419249e-08	- CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.589 RNASLOpt: 0.575 Sensitivity CRWrnafold: 0.521 RNASLOpt: 0.486 Positive Predictive Value CRWrnafold: 0.672 RNASLOpt: 0.688 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 8.64649098287e-07	+ RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.537 Pknots: 0.491 Sensitivity RNASLOpt: 0.435 Pknots: 0.445 Positive Predictive Value RNASLOpt: 0.671 Pknots: 0.549 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.425 RNASampler(seed): 0.317 Sensitivity RNASLOpt: 0.372 RNASampler(seed): 0.207 Positive Predictive Value RNASLOpt: 0.491 RNASampler(seed): 0.492 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	- Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.601 RNASLOpt: 0.567 Sensitivity Alterna: 0.537 RNASLOpt: 0.458 Positive Predictive Value Alterna: 0.684 RNASLOpt: 0.713 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Mastr(20): 0.475 Sensitivity RNASLOpt: 0.443 Mastr(20): 0.308 Positive Predictive Value RNASLOpt: 0.664 Mastr(20): 0.740 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.552 Vsfold4: 0.500 Sensitivity RNASLOpt: 0.447 Vsfold4: 0.418 Positive Predictive Value RNASLOpt: 0.688 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.426 Murlet(seed): 0.400 Sensitivity RNASLOpt: 0.352 Murlet(seed): 0.225 Positive Predictive Value RNASLOpt: 0.523 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.553 Vsfold5: 0.433 Sensitivity RNASLOpt: 0.462 Vsfold5: 0.373 Positive Predictive Value RNASLOpt: 0.669 Vsfold5: 0.510 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.505 MCFold: 0.450 Sensitivity RNASLOpt: 0.414 MCFold: 0.460 Positive Predictive Value RNASLOpt: 0.622 MCFold: 0.448 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.610 RDfolder: 0.491 Sensitivity RNASLOpt: 0.504 RDfolder: 0.389 Positive Predictive Value RNASLOpt: 0.747 RDfolder: 0.632 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.488 RNAwolf: 0.366 Sensitivity RNASLOpt: 0.395 RNAwolf: 0.342 Positive Predictive Value RNASLOpt: 0.607 RNAwolf: 0.397 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.635 CMfinder(20): 0.546 Sensitivity RNASLOpt: 0.512 CMfinder(20): 0.366 Positive Predictive Value RNASLOpt: 0.792 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.530 NanoFolder: 0.339 Sensitivity RNASLOpt: 0.424 NanoFolder: 0.350 Positive Predictive Value RNASLOpt: 0.669 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.477 RNASLOpt: 0.400 Sensitivity Multilign(seed): 0.358 RNASLOpt: 0.316 Positive Predictive Value Multilign(seed): 0.642 RNASLOpt: 0.513 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.533 PPfold(seed): 0.100 Sensitivity RNASLOpt: 0.431 PPfold(seed): 0.019 Positive Predictive Value RNASLOpt: 0.666 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 RSpredict(seed): 0.115 Sensitivity RNASLOpt: 0.413 RSpredict(seed): 0.046 Positive Predictive Value RNASLOpt: 0.615 RSpredict(seed): 0.294 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.462 Carnac(seed): 0.107 Sensitivity RNASLOpt: 0.378 Carnac(seed): 0.012 Positive Predictive Value RNASLOpt: 0.572 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.533 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.431 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.666 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.48055519165e-08	? CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNASLOpt: 0.625 Sensitivity PETfold_2.0(seed): 0.642 RNASLOpt: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 RNASLOpt: 0.797 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASLOpt: 0.456 Sensitivity PETfold_2.0(20): 0.509 RNASLOpt: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 RNASLOpt: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Cylofold	20 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.720 Cylofold: 0.608 Sensitivity CentroidAlifold(20): 0.566 Cylofold: 0.524 Positive Predictive Value CentroidAlifold(20): 0.919 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Cylofold: 0.563 Sensitivity PETfold_pre2.0(seed): 0.609 Cylofold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.871 Cylofold: 0.681 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	35 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.675 Cylofold: 0.522 Sensitivity ContextFold: 0.562 Cylofold: 0.436 Positive Predictive Value ContextFold: 0.814 Cylofold: 0.632 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.677 Cylofold: 0.617 Sensitivity MXScarna(seed): 0.568 Cylofold: 0.527 Positive Predictive Value MXScarna(seed): 0.811 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	19 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.701 Cylofold: 0.616 Sensitivity RNAalifold(20): 0.543 Cylofold: 0.528 Positive Predictive Value RNAalifold(20): 0.909 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.26346675981e-08	9 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Cylofold: 0.611 Sensitivity PETfold_pre2.0(20): 0.624 Cylofold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.896 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.756 Cylofold: 0.664 Sensitivity PPfold(20): 0.610 Cylofold: 0.559 Positive Predictive Value PPfold(20): 0.941 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	42 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.642 Cylofold: 0.533 Sensitivity IPknot: 0.540 Cylofold: 0.447 Positive Predictive Value IPknot: 0.771 Cylofold: 0.644 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 Cylofold: 0.611 Sensitivity CentroidAlifold(seed): 0.417 Cylofold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.928 Cylofold: 0.719 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0417598136925	19 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.673 Cylofold: 0.616 Sensitivity RNASampler(20): 0.507 Cylofold: 0.528 Positive Predictive Value RNASampler(20): 0.896 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	12 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.725 Cylofold: 0.664 Sensitivity TurboFold(20): 0.590 Cylofold: 0.559 Positive Predictive Value TurboFold(20): 0.895 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	19 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.681 Cylofold: 0.616 Sensitivity MXScarna(20): 0.566 Cylofold: 0.528 Positive Predictive Value MXScarna(20): 0.822 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	75 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.607 Sensitivity Sfold: 0.563 Cylofold: 0.517 Positive Predictive Value Sfold: 0.772 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.591 Cylofold: 0.534 Sensitivity CentroidHomfold‑LAST: 0.451 Cylofold: 0.448 Positive Predictive Value CentroidHomfold‑LAST: 0.781 Cylofold: 0.645 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.672 Cylofold: 0.607 Sensitivity Contrafold: 0.597 Cylofold: 0.517 Positive Predictive Value Contrafold: 0.761 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.592 RNAalifold(seed): 0.589 Sensitivity Cylofold: 0.506 RNAalifold(seed): 0.398 Positive Predictive Value Cylofold: 0.700 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.068096332007	75 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.652 Cylofold: 0.607 Sensitivity HotKnots: 0.584 Cylofold: 0.517 Positive Predictive Value HotKnots: 0.734 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.651 Cylofold: 0.607 Sensitivity MaxExpect: 0.574 Cylofold: 0.517 Positive Predictive Value MaxExpect: 0.744 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.653 Cylofold: 0.603 Sensitivity CentroidFold: 0.564 Cylofold: 0.515 Positive Predictive Value CentroidFold: 0.763 Cylofold: 0.713 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.637 Cylofold: 0.607 Sensitivity UNAFold: 0.566 Cylofold: 0.517 Positive Predictive Value UNAFold: 0.724 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.639 Cylofold: 0.607 Sensitivity PknotsRG: 0.572 Cylofold: 0.517 Positive Predictive Value PknotsRG: 0.721 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.641 Cylofold: 0.603 Sensitivity ProbKnot: 0.580 Cylofold: 0.513 Positive Predictive Value ProbKnot: 0.715 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.638 Cylofold: 0.616 Sensitivity Murlet(20): 0.481 Cylofold: 0.528 Positive Predictive Value Murlet(20): 0.851 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	75 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.636 Cylofold: 0.607 Sensitivity RNAfold: 0.566 Cylofold: 0.517 Positive Predictive Value RNAfold: 0.721 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.616 Carnac(20): 0.593 Sensitivity Cylofold: 0.528 Carnac(20): 0.392 Positive Predictive Value Cylofold: 0.725 Carnac(20): 0.902 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	75 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.639 Cylofold: 0.607 Sensitivity RNAshapes: 0.566 Cylofold: 0.517 Positive Predictive Value RNAshapes: 0.727 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.659 Cylofold: 0.607 Sensitivity Fold: 0.589 Cylofold: 0.517 Positive Predictive Value Fold: 0.742 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.620 TurboFold(seed): 0.613 Sensitivity Cylofold: 0.504 TurboFold(seed): 0.487 Positive Predictive Value Cylofold: 0.770 TurboFold(seed): 0.779 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	20 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.608 RSpredict(20): 0.589 Sensitivity Cylofold: 0.524 RSpredict(20): 0.451 Positive Predictive Value Cylofold: 0.711 RSpredict(20): 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.61189297362e-07	50 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.658 Cylofold: 0.611 Sensitivity Afold: 0.597 Cylofold: 0.525 Positive Predictive Value Afold: 0.731 Cylofold: 0.717 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.647 Cylofold: 0.607 Sensitivity RNAsubopt: 0.576 Cylofold: 0.517 Positive Predictive Value RNAsubopt: 0.733 Cylofold: 0.718 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.539 Cylofold: 0.522 Sensitivity RNASLOpt: 0.445 Cylofold: 0.436 Positive Predictive Value RNASLOpt: 0.658 Cylofold: 0.632 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08		- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.650 Cylofold: 0.604 Sensitivity McQFold: 0.557 Cylofold: 0.514 Positive Predictive Value McQFold: 0.765 Cylofold: 0.716 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.604 Multilign(20): 0.583 Sensitivity Cylofold: 0.514 Multilign(20): 0.475 Positive Predictive Value Cylofold: 0.716 Multilign(20): 0.724 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.12267791166e-06	= CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.569 Cylofold: 0.562 Sensitivity CRWrnafold: 0.497 Cylofold: 0.482 Positive Predictive Value CRWrnafold: 0.660 Cylofold: 0.665 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.00516288448633	- Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.645 Cylofold: 0.637 Sensitivity Pknots: 0.578 Cylofold: 0.546 Positive Predictive Value Pknots: 0.726 Cylofold: 0.750 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.82713256396e-06	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.659 RNASampler(seed): 0.601 Sensitivity Cylofold: 0.579 RNASampler(seed): 0.433 Positive Predictive Value Cylofold: 0.755 RNASampler(seed): 0.839 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.700 Alterna: 0.671 Sensitivity Cylofold: 0.608 Alterna: 0.613 Positive Predictive Value Cylofold: 0.813 Alterna: 0.743 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.616 Mastr(20): 0.553 Sensitivity Cylofold: 0.528 Mastr(20): 0.381 Positive Predictive Value Cylofold: 0.725 Mastr(20): 0.809 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.612 Vsfold4: 0.563 Sensitivity Cylofold: 0.524 Vsfold4: 0.477 Positive Predictive Value Cylofold: 0.722 Vsfold4: 0.673 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.579 Murlet(seed): 0.479 Sensitivity Cylofold: 0.492 Murlet(seed): 0.287 Positive Predictive Value Cylofold: 0.687 Murlet(seed): 0.806 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.605 Vsfold5: 0.511 Sensitivity Cylofold: 0.516 Vsfold5: 0.442 Positive Predictive Value Cylofold: 0.716 Vsfold5: 0.599 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.641 MCFold: 0.543 Sensitivity Cylofold: 0.550 MCFold: 0.562 Positive Predictive Value Cylofold: 0.754 MCFold: 0.532 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.696 RDfolder: 0.582 Sensitivity Cylofold: 0.605 RDfolder: 0.487 Positive Predictive Value Cylofold: 0.809 RDfolder: 0.706 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.529 RNAwolf: 0.433 Sensitivity Cylofold: 0.445 RNAwolf: 0.403 Positive Predictive Value Cylofold: 0.637 RNAwolf: 0.474 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.631 CMfinder(20): 0.546 Sensitivity Cylofold: 0.518 CMfinder(20): 0.366 Positive Predictive Value Cylofold: 0.773 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.528 NanoFolder: 0.380 Sensitivity Cylofold: 0.447 NanoFolder: 0.387 Positive Predictive Value Cylofold: 0.631 NanoFolder: 0.383 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.590 Cylofold: 0.541 Sensitivity Multilign(seed): 0.470 Cylofold: 0.436 Positive Predictive Value Multilign(seed): 0.748 Cylofold: 0.680 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.594 PPfold(seed): 0.091 Sensitivity Cylofold: 0.490 PPfold(seed): 0.011 Positive Predictive Value Cylofold: 0.727 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.611 RSpredict(seed): 0.231 Sensitivity Cylofold: 0.523 RSpredict(seed): 0.109 Positive Predictive Value Cylofold: 0.719 RSpredict(seed): 0.500 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.601 Carnac(seed): 0.193 Sensitivity Cylofold: 0.510 Carnac(seed): 0.037 Positive Predictive Value Cylofold: 0.715 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.617 Mastr(seed): 0.223 Sensitivity Cylofold: 0.527 Mastr(seed): 0.050 Positive Predictive Value Cylofold: 0.729 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
McQFold	39 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.673 McQFold: 0.508 Sensitivity CentroidAlifold(20): 0.516 McQFold: 0.437 Positive Predictive Value CentroidAlifold(20): 0.879 McQFold: 0.596 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 McQFold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.602 McQFold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.850 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	48 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.560 McQFold: 0.392 Sensitivity ContextFold: 0.463 McQFold: 0.333 Positive Predictive Value ContextFold: 0.679 McQFold: 0.462 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.667 McQFold: 0.544 Sensitivity MXScarna(seed): 0.560 McQFold: 0.471 Positive Predictive Value MXScarna(seed): 0.794 McQFold: 0.629 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.656 McQFold: 0.539 Sensitivity RNAalifold(20): 0.502 McQFold: 0.462 Positive Predictive Value RNAalifold(20): 0.860 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 McQFold: 0.449 Sensitivity PETfold_pre2.0(20): 0.530 McQFold: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.51155234096e-08	15 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.691 McQFold: 0.583 Sensitivity PPfold(20): 0.544 McQFold: 0.491 Positive Predictive Value PPfold(20): 0.881 McQFold: 0.697 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	56 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.552 McQFold: 0.410 Sensitivity IPknot: 0.445 McQFold: 0.348 Positive Predictive Value IPknot: 0.685 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 McQFold: 0.529 Sensitivity CentroidAlifold(seed): 0.443 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.880 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.623 McQFold: 0.539 Sensitivity RNASampler(20): 0.470 McQFold: 0.462 Positive Predictive Value RNASampler(20): 0.830 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.655 McQFold: 0.583 Sensitivity TurboFold(20): 0.529 McQFold: 0.491 Positive Predictive Value TurboFold(20): 0.816 McQFold: 0.697 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	34 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.624 McQFold: 0.539 Sensitivity MXScarna(20): 0.518 McQFold: 0.462 Positive Predictive Value MXScarna(20): 0.756 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	139 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.508 McQFold: 0.415 Sensitivity Sfold: 0.431 McQFold: 0.332 Positive Predictive Value Sfold: 0.598 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.587 McQFold: 0.538 Sensitivity CentroidHomfold‑LAST: 0.439 McQFold: 0.453 Positive Predictive Value CentroidHomfold‑LAST: 0.789 McQFold: 0.644 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.541 McQFold: 0.415 Sensitivity Contrafold: 0.476 McQFold: 0.332 Positive Predictive Value Contrafold: 0.616 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 McQFold: 0.536 Sensitivity RNAalifold(seed): 0.460 McQFold: 0.469 Positive Predictive Value RNAalifold(seed): 0.866 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.621 McQFold: 0.571 Sensitivity HotKnots: 0.557 McQFold: 0.492 Positive Predictive Value HotKnots: 0.697 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.551 McQFold: 0.454 Sensitivity MaxExpect: 0.479 McQFold: 0.388 Positive Predictive Value MaxExpect: 0.634 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	136 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.528 McQFold: 0.432 Sensitivity CentroidFold: 0.441 McQFold: 0.345 Positive Predictive Value CentroidFold: 0.633 McQFold: 0.541 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.488 McQFold: 0.415 Sensitivity UNAFold: 0.434 McQFold: 0.332 Positive Predictive Value UNAFold: 0.549 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	138 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.477 McQFold: 0.410 Sensitivity PknotsRG: 0.429 McQFold: 0.327 Positive Predictive Value PknotsRG: 0.531 McQFold: 0.516 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.535 McQFold: 0.482 Sensitivity ProbKnot: 0.478 McQFold: 0.416 Positive Predictive Value ProbKnot: 0.599 McQFold: 0.559 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.577 McQFold: 0.539 Sensitivity Murlet(20): 0.423 McQFold: 0.462 Positive Predictive Value Murlet(20): 0.791 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.6410608252e-08	139 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.483 McQFold: 0.415 Sensitivity RNAfold: 0.433 McQFold: 0.332 Positive Predictive Value RNAfold: 0.540 McQFold: 0.518 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.577 McQFold: 0.539 Sensitivity Carnac(20): 0.372 McQFold: 0.462 Positive Predictive Value Carnac(20): 0.897 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	134 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.601 McQFold: 0.571 Sensitivity RNAshapes: 0.532 McQFold: 0.492 Positive Predictive Value RNAshapes: 0.683 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	100 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.533 McQFold: 0.495 Sensitivity Fold: 0.479 McQFold: 0.426 Positive Predictive Value Fold: 0.595 McQFold: 0.576 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.544 McQFold: 0.527 Sensitivity TurboFold(seed): 0.439 McQFold: 0.450 Positive Predictive Value TurboFold(seed): 0.679 McQFold: 0.623 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000799494419018	39 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.544 McQFold: 0.513 Sensitivity RSpredict(20): 0.425 McQFold: 0.445 Positive Predictive Value RSpredict(20): 0.701 McQFold: 0.597 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.467 McQFold: 0.391 Sensitivity Afold: 0.423 McQFold: 0.309 Positive Predictive Value Afold: 0.516 McQFold: 0.495 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.594 McQFold: 0.571 Sensitivity RNAsubopt: 0.533 McQFold: 0.492 Positive Predictive Value RNAsubopt: 0.666 McQFold: 0.668 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.483 McQFold: 0.474 Sensitivity RNASLOpt: 0.387 McQFold: 0.401 Positive Predictive Value RNASLOpt: 0.608 McQFold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 9.69999390915e-05	74 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.650 Cylofold: 0.604 Sensitivity McQFold: 0.557 Cylofold: 0.514 Positive Predictive Value McQFold: 0.765 Cylofold: 0.716 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.587 Multilign(20): 0.561 Sensitivity McQFold: 0.499 Multilign(20): 0.466 Positive Predictive Value McQFold: 0.696 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 6.99159849967e-08	= McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.585 CRWrnafold: 0.576 Sensitivity McQFold: 0.505 CRWrnafold: 0.513 Positive Predictive Value McQFold: 0.685 CRWrnafold: 0.654 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00374085173498	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.621 Pknots: 0.599 Sensitivity McQFold: 0.534 Pknots: 0.543 Positive Predictive Value McQFold: 0.729 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.635 McQFold: 0.628 Sensitivity RNASampler(seed): 0.484 McQFold: 0.562 Positive Predictive Value RNASampler(seed): 0.837 McQFold: 0.707 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.0398923262603	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.700 Alterna: 0.665 Sensitivity McQFold: 0.600 Alterna: 0.599 Positive Predictive Value McQFold: 0.826 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.539 Mastr(20): 0.514 Sensitivity McQFold: 0.462 Mastr(20): 0.339 Positive Predictive Value McQFold: 0.633 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.599 Vsfold4: 0.545 Sensitivity McQFold: 0.519 Vsfold4: 0.463 Positive Predictive Value McQFold: 0.696 Vsfold4: 0.648 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.627 Murlet(seed): 0.514 Sensitivity McQFold: 0.544 Murlet(seed): 0.315 Positive Predictive Value McQFold: 0.728 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.604 Vsfold5: 0.507 Sensitivity McQFold: 0.523 Vsfold5: 0.439 Positive Predictive Value McQFold: 0.705 Vsfold5: 0.594 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.611 MCFold: 0.519 Sensitivity McQFold: 0.528 MCFold: 0.533 Positive Predictive Value McQFold: 0.713 MCFold: 0.514 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.697 RDfolder: 0.592 Sensitivity McQFold: 0.596 RDfolder: 0.491 Positive Predictive Value McQFold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.420 RNAwolf: 0.353 Sensitivity McQFold: 0.357 RNAwolf: 0.328 Positive Predictive Value McQFold: 0.495 RNAwolf: 0.382 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: 0.664 CMfinder(20): 0.546 Sensitivity McQFold: 0.530 CMfinder(20): 0.366 Positive Predictive Value McQFold: 0.837 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.493 NanoFolder: 0.327 Sensitivity McQFold: 0.424 NanoFolder: 0.338 Positive Predictive Value McQFold: 0.581 NanoFolder: 0.326 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.575 Multilign(seed): 0.558 Sensitivity McQFold: 0.472 Multilign(seed): 0.434 Positive Predictive Value McQFold: 0.707 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.568 PPfold(seed): 0.092 Sensitivity McQFold: 0.475 PPfold(seed): 0.016 Positive Predictive Value McQFold: 0.686 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.531 RSpredict(seed): 0.375 Sensitivity McQFold: 0.462 RSpredict(seed): 0.220 Positive Predictive Value McQFold: 0.613 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.554 Carnac(seed): 0.404 Sensitivity McQFold: 0.479 Carnac(seed): 0.181 Positive Predictive Value McQFold: 0.643 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.563 Mastr(seed): 0.236 Sensitivity McQFold: 0.489 Mastr(seed): 0.062 Positive Predictive Value McQFold: 0.652 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 McQFold: 0.616 Sensitivity PETfold_2.0(seed): 0.642 McQFold: 0.453 Positive Predictive Value PETfold_2.0(seed): 0.924 McQFold: 0.843 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 McQFold: 0.491 Sensitivity PETfold_2.0(20): 0.509 McQFold: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 McQFold: 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(20)	21 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Multilign(20): 0.526 Sensitivity CentroidAlifold(20): 0.518 Multilign(20): 0.437 Positive Predictive Value CentroidAlifold(20): 0.879 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(seed): 0.616 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	10 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.706 Multilign(20): 0.557 Sensitivity ContextFold: 0.565 Multilign(20): 0.472 Positive Predictive Value ContextFold: 0.885 Multilign(20): 0.663 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	15 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.658 Multilign(20): 0.561 Sensitivity MXScarna(seed): 0.543 Multilign(20): 0.466 Positive Predictive Value MXScarna(seed): 0.801 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	15 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.666 Multilign(20): 0.561 Sensitivity RNAalifold(20): 0.511 Multilign(20): 0.466 Positive Predictive Value RNAalifold(20): 0.875 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	16 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(20): 0.564 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.825 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.10198558684e-08	14 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.723 Multilign(20): 0.596 Sensitivity PPfold(20): 0.581 Multilign(20): 0.507 Positive Predictive Value PPfold(20): 0.905 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	13 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.620 Multilign(20): 0.577 Sensitivity IPknot: 0.516 Multilign(20): 0.488 Positive Predictive Value IPknot: 0.749 Multilign(20): 0.688 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	21 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.576 Multilign(20): 0.526 Sensitivity CentroidAlifold(seed): 0.359 Multilign(20): 0.437 Positive Predictive Value CentroidAlifold(seed): 0.927 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.54865340847e-08	15 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.638 Multilign(20): 0.561 Sensitivity RNASampler(20): 0.474 Multilign(20): 0.466 Positive Predictive Value RNASampler(20): 0.863 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	14 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.681 Multilign(20): 0.596 Sensitivity TurboFold(20): 0.558 Multilign(20): 0.507 Positive Predictive Value TurboFold(20): 0.836 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	15 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.644 Multilign(20): 0.561 Sensitivity MXScarna(20): 0.538 Multilign(20): 0.466 Positive Predictive Value MXScarna(20): 0.777 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	15 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.598 Multilign(20): 0.561 Sensitivity Sfold: 0.501 Multilign(20): 0.466 Positive Predictive Value Sfold: 0.720 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	14 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Multilign(20): 0.596 Sensitivity CentroidHomfold‑LAST: 0.549 Multilign(20): 0.507 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Multilign(20): 0.706 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	15 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.576 Multilign(20): 0.561 Sensitivity Contrafold: 0.505 Multilign(20): 0.466 Positive Predictive Value Contrafold: 0.663 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.99999654892e-06	9 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 Multilign(20): 0.431 Sensitivity RNAalifold(seed): 0.375 Multilign(20): 0.346 Positive Predictive Value RNAalifold(seed): 0.938 Multilign(20): 0.544 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	15 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.599 Multilign(20): 0.561 Sensitivity HotKnots: 0.524 Multilign(20): 0.466 Positive Predictive Value HotKnots: 0.690 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	15 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.561 MaxExpect: 0.547 Sensitivity Multilign(20): 0.466 MaxExpect: 0.476 Positive Predictive Value Multilign(20): 0.682 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	21 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.526 CentroidFold: 0.472 Sensitivity Multilign(20): 0.437 CentroidFold: 0.406 Positive Predictive Value Multilign(20): 0.640 CentroidFold: 0.556 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	15 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.569 Multilign(20): 0.561 Sensitivity UNAFold: 0.495 Multilign(20): 0.466 Positive Predictive Value UNAFold: 0.661 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.83111007457e-05	15 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.602 Multilign(20): 0.561 Sensitivity PknotsRG: 0.530 Multilign(20): 0.466 Positive Predictive Value PknotsRG: 0.691 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	15 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.561 ProbKnot: 0.556 Sensitivity Multilign(20): 0.466 ProbKnot: 0.493 Positive Predictive Value Multilign(20): 0.682 ProbKnot: 0.634 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.83239157526e-05	15 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.576 Multilign(20): 0.561 Sensitivity Murlet(20): 0.430 Multilign(20): 0.466 Positive Predictive Value Murlet(20): 0.780 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.88034995625e-07	15 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.580 Multilign(20): 0.561 Sensitivity RNAfold: 0.505 Multilign(20): 0.466 Positive Predictive Value RNAfold: 0.672 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	15 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.561 Carnac(20): 0.549 Sensitivity Multilign(20): 0.466 Carnac(20): 0.356 Positive Predictive Value Multilign(20): 0.682 Carnac(20): 0.853 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.76858620702e-06	15 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.624 Multilign(20): 0.561 Sensitivity RNAshapes: 0.543 Multilign(20): 0.466 Positive Predictive Value RNAshapes: 0.723 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.601 Multilign(20): 0.561 Sensitivity Fold: 0.530 Multilign(20): 0.466 Positive Predictive Value Fold: 0.688 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.70180496535e-08	8 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Multilign(20): 0.568 Sensitivity TurboFold(seed): 0.490 Multilign(20): 0.483 Positive Predictive Value TurboFold(seed): 0.729 Multilign(20): 0.676 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	21 RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.535 Multilign(20): 0.526 Sensitivity RSpredict(20): 0.405 Multilign(20): 0.437 Positive Predictive Value RSpredict(20): 0.712 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.000406393755088	6 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.555 Multilign(20): 0.500 Sensitivity Afold: 0.497 Multilign(20): 0.416 Positive Predictive Value Afold: 0.624 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	15 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.590 Multilign(20): 0.561 Sensitivity RNAsubopt: 0.518 Multilign(20): 0.466 Positive Predictive Value RNAsubopt: 0.678 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	10 RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.580 Multilign(20): 0.557 Sensitivity RNASLOpt: 0.477 Multilign(20): 0.472 Positive Predictive Value RNASLOpt: 0.710 Multilign(20): 0.663 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.76965419249e-08	13 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.604 Multilign(20): 0.583 Sensitivity Cylofold: 0.514 Multilign(20): 0.475 Positive Predictive Value Cylofold: 0.716 Multilign(20): 0.724 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.12267791166e-06	15 McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.587 Multilign(20): 0.561 Sensitivity McQFold: 0.499 Multilign(20): 0.466 Positive Predictive Value McQFold: 0.696 Multilign(20): 0.682 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 6.99159849967e-08		? CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Multilign(20): 0.509 Sensitivity CRWrnafold: 0.483 Multilign(20): 0.432 Positive Predictive Value CRWrnafold: 0.623 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.561 Pknots: 0.532 Sensitivity Multilign(20): 0.466 Pknots: 0.468 Positive Predictive Value Multilign(20): 0.682 Pknots: 0.612 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39442331656e-08	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.581 Multilign(20): 0.559 Sensitivity RNASampler(seed): 0.426 Multilign(20): 0.504 Positive Predictive Value RNASampler(seed): 0.797 Multilign(20): 0.625 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.706 Alterna: 0.654 Sensitivity Multilign(20): 0.610 Alterna: 0.569 Positive Predictive Value Multilign(20): 0.824 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.561 Mastr(20): 0.554 Sensitivity Multilign(20): 0.466 Mastr(20): 0.389 Positive Predictive Value Multilign(20): 0.682 Mastr(20): 0.795 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000912413615127	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.561 Vsfold4: 0.490 Sensitivity Multilign(20): 0.466 Vsfold4: 0.407 Positive Predictive Value Multilign(20): 0.682 Vsfold4: 0.599 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.460 Multilign(20): 0.431 Sensitivity Murlet(seed): 0.258 Multilign(20): 0.346 Positive Predictive Value Murlet(seed): 0.830 Multilign(20): 0.544 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.561 Vsfold5: 0.431 Sensitivity Multilign(20): 0.466 Vsfold5: 0.368 Positive Predictive Value Multilign(20): 0.682 Vsfold5: 0.513 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.512 MCFold: 0.413 Sensitivity Multilign(20): 0.425 MCFold: 0.426 Positive Predictive Value Multilign(20): 0.623 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.623 RDfolder: 0.511 Sensitivity Multilign(20): 0.519 RDfolder: 0.386 Positive Predictive Value Multilign(20): 0.756 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.534 RNAwolf: 0.366 Sensitivity Multilign(20): 0.449 RNAwolf: 0.345 Positive Predictive Value Multilign(20): 0.642 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.578 CMfinder(20): 0.546 Sensitivity Multilign(20): 0.482 CMfinder(20): 0.366 Positive Predictive Value Multilign(20): 0.699 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.610 NanoFolder: 0.276 Sensitivity Multilign(20): 0.524 NanoFolder: 0.286 Positive Predictive Value Multilign(20): 0.715 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Multilign(20): 0.661 Sensitivity Multilign(seed): 0.543 Multilign(20): 0.551 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.800 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.577 PPfold(seed): 0.020 Sensitivity Multilign(20): 0.488 PPfold(seed): 0.002 Positive Predictive Value Multilign(20): 0.688 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.526 RSpredict(seed): 0.170 Sensitivity Multilign(20): 0.437 RSpredict(seed): 0.067 Positive Predictive Value Multilign(20): 0.640 RSpredict(seed): 0.439 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.476 Carnac(seed): 0.237 Sensitivity Multilign(20): 0.386 Carnac(seed): 0.056 Positive Predictive Value Multilign(20): 0.596 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.01499922709e-08	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.561 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.466 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.682 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	? CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CRWrnafold	7 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.687 CRWrnafold: 0.546 Sensitivity CentroidAlifold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value CentroidAlifold(20): 0.924 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.675 CRWrnafold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.553 CRWrnafold: 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.828 CRWrnafold: 0.599 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	26 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.690 CRWrnafold: 0.589 Sensitivity ContextFold: 0.579 CRWrnafold: 0.521 Positive Predictive Value ContextFold: 0.827 CRWrnafold: 0.672 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	9 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.610 CRWrnafold: 0.536 Sensitivity MXScarna(seed): 0.490 CRWrnafold: 0.472 Positive Predictive Value MXScarna(seed): 0.765 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.620 CRWrnafold: 0.546 Sensitivity RNAalifold(20): 0.479 CRWrnafold: 0.483 Positive Predictive Value RNAalifold(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CRWrnafold: 0.531 Sensitivity PETfold_pre2.0(20): 0.497 CRWrnafold: 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 CRWrnafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.657 CRWrnafold: 0.546 Sensitivity PPfold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value PPfold(20): 0.846 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.654 CRWrnafold: 0.585 Sensitivity IPknot: 0.559 CRWrnafold: 0.522 Positive Predictive Value IPknot: 0.773 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.578 CRWrnafold: 0.536 Sensitivity CentroidAlifold(seed): 0.343 CRWrnafold: 0.472 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.618 CRWrnafold: 0.546 Sensitivity RNASampler(20): 0.462 CRWrnafold: 0.483 Positive Predictive Value RNASampler(20): 0.832 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.570 CRWrnafold: 0.546 Sensitivity TurboFold(20): 0.453 CRWrnafold: 0.483 Positive Predictive Value TurboFold(20): 0.723 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.569 CRWrnafold: 0.546 Sensitivity MXScarna(20): 0.466 CRWrnafold: 0.483 Positive Predictive Value MXScarna(20): 0.701 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.618 CRWrnafold: 0.585 Sensitivity Sfold: 0.530 CRWrnafold: 0.522 Positive Predictive Value Sfold: 0.728 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 CRWrnafold: 0.576 Sensitivity CentroidHomfold‑LAST: 0.501 CRWrnafold: 0.513 Positive Predictive Value CentroidHomfold‑LAST: 0.845 CRWrnafold: 0.654 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.636 CRWrnafold: 0.585 Sensitivity Contrafold: 0.559 CRWrnafold: 0.522 Positive Predictive Value Contrafold: 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.500 CRWrnafold: 0.419 Sensitivity RNAalifold(seed): 0.320 CRWrnafold: 0.377 Positive Predictive Value RNAalifold(seed): 0.789 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	32 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.626 CRWrnafold: 0.585 Sensitivity HotKnots: 0.569 CRWrnafold: 0.522 Positive Predictive Value HotKnots: 0.695 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.585 MaxExpect: 0.576 Sensitivity CRWrnafold: 0.522 MaxExpect: 0.511 Positive Predictive Value CRWrnafold: 0.663 MaxExpect: 0.656 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.47427610203e-05	32 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.639 CRWrnafold: 0.585 Sensitivity CentroidFold: 0.545 CRWrnafold: 0.522 Positive Predictive Value CentroidFold: 0.757 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.590 CRWrnafold: 0.585 Sensitivity UNAFold: 0.530 CRWrnafold: 0.522 Positive Predictive Value UNAFold: 0.664 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.288298117014	32 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.621 CRWrnafold: 0.585 Sensitivity PknotsRG: 0.563 CRWrnafold: 0.522 Positive Predictive Value PknotsRG: 0.692 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.585 ProbKnot: 0.580 Sensitivity CRWrnafold: 0.522 ProbKnot: 0.531 Positive Predictive Value CRWrnafold: 0.663 ProbKnot: 0.640 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.91710725109e-05	7 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.568 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.428 CRWrnafold: 0.483 Positive Predictive Value Murlet(20): 0.759 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.610 CRWrnafold: 0.585 Sensitivity RNAfold: 0.545 CRWrnafold: 0.522 Positive Predictive Value RNAfold: 0.691 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 8.81311508309e-08	7 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Carnac(20): 0.526 Sensitivity CRWrnafold: 0.483 Carnac(20): 0.335 Positive Predictive Value CRWrnafold: 0.623 Carnac(20): 0.832 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.609 CRWrnafold: 0.585 Sensitivity RNAshapes: 0.542 CRWrnafold: 0.522 Positive Predictive Value RNAshapes: 0.691 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 6.54014656494e-08	32 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.585 Fold: 0.573 Sensitivity CRWrnafold: 0.522 Fold: 0.514 Positive Predictive Value CRWrnafold: 0.663 Fold: 0.645 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	7 CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 TurboFold(seed): 0.483 Sensitivity CRWrnafold: 0.428 TurboFold(seed): 0.397 Positive Predictive Value CRWrnafold: 0.554 TurboFold(seed): 0.595 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.546 RSpredict(20): 0.446 Sensitivity CRWrnafold: 0.483 RSpredict(20): 0.331 Positive Predictive Value CRWrnafold: 0.623 RSpredict(20): 0.609 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	19 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.638 CRWrnafold: 0.564 Sensitivity Afold: 0.592 CRWrnafold: 0.515 Positive Predictive Value Afold: 0.695 CRWrnafold: 0.627 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	32 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.585 RNAsubopt: 0.583 Sensitivity CRWrnafold: 0.522 RNAsubopt: 0.524 Positive Predictive Value CRWrnafold: 0.663 RNAsubopt: 0.656 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.19883461079e-06	26 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.589 RNASLOpt: 0.575 Sensitivity CRWrnafold: 0.521 RNASLOpt: 0.486 Positive Predictive Value CRWrnafold: 0.672 RNASLOpt: 0.688 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 8.64649098287e-07	25 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.569 Cylofold: 0.562 Sensitivity CRWrnafold: 0.497 Cylofold: 0.482 Positive Predictive Value CRWrnafold: 0.660 Cylofold: 0.665 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.00516288448633	31 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.585 CRWrnafold: 0.576 Sensitivity McQFold: 0.505 CRWrnafold: 0.513 Positive Predictive Value McQFold: 0.685 CRWrnafold: 0.654 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00374085173498	7 CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Multilign(20): 0.509 Sensitivity CRWrnafold: 0.483 Multilign(20): 0.432 Positive Predictive Value CRWrnafold: 0.623 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		+ CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.585 Pknots: 0.545 Sensitivity CRWrnafold: 0.522 Pknots: 0.498 Positive Predictive Value CRWrnafold: 0.663 Pknots: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.357 CRWrnafold: 0.262 Sensitivity RNASampler(seed): 0.253 CRWrnafold: 0.253 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.279 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.593 Alterna: 0.586 Sensitivity CRWrnafold: 0.535 Alterna: 0.535 Positive Predictive Value CRWrnafold: 0.668 Alterna: 0.654 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000144846895958	? Mastr(20) vs CRWrnafold Matthews Correlation Coefficient Mastr(20): 0.547 CRWrnafold: 0.546 Sensitivity Mastr(20): 0.373 CRWrnafold: 0.483 Positive Predictive Value Mastr(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.585 Vsfold4: 0.502 Sensitivity CRWrnafold: 0.522 Vsfold4: 0.431 Positive Predictive Value CRWrnafold: 0.663 Vsfold4: 0.595 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.435 CRWrnafold: 0.419 Sensitivity Murlet(seed): 0.251 CRWrnafold: 0.377 Positive Predictive Value Murlet(seed): 0.759 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.580 Vsfold5: 0.454 Sensitivity CRWrnafold: 0.517 Vsfold5: 0.398 Positive Predictive Value CRWrnafold: 0.659 Vsfold5: 0.528 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.585 MCFold: 0.547 Sensitivity CRWrnafold: 0.525 MCFold: 0.579 Positive Predictive Value CRWrnafold: 0.659 MCFold: 0.525 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.613 RDfolder: 0.465 Sensitivity CRWrnafold: 0.544 RDfolder: 0.365 Positive Predictive Value CRWrnafold: 0.701 RDfolder: 0.606 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.585 RNAwolf: 0.475 Sensitivity CRWrnafold: 0.522 RNAwolf: 0.449 Positive Predictive Value CRWrnafold: 0.663 RNAwolf: 0.513 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.584 NanoFolder: 0.475 Sensitivity CRWrnafold: 0.519 NanoFolder: 0.484 Positive Predictive Value CRWrnafold: 0.664 NanoFolder: 0.474 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.465 CRWrnafold: 0.443 Sensitivity Multilign(seed): 0.365 CRWrnafold: 0.375 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 PPfold(seed): 0.114 Sensitivity CRWrnafold: 0.472 PPfold(seed): 0.024 Positive Predictive Value CRWrnafold: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 RSpredict(seed): 0.108 Sensitivity CRWrnafold: 0.472 RSpredict(seed): 0.042 Positive Predictive Value CRWrnafold: 0.616 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 Carnac(seed): 0.132 Sensitivity CRWrnafold: 0.428 Carnac(seed): 0.017 Positive Predictive Value CRWrnafold: 0.554 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.472 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.616 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Pknots	38 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Pknots: 0.483 Sensitivity CentroidAlifold(20): 0.529 Pknots: 0.439 Positive Predictive Value CentroidAlifold(20): 0.879 Pknots: 0.539 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Pknots: 0.457 Sensitivity PETfold_pre2.0(seed): 0.595 Pknots: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.642 Pknots: 0.491 Sensitivity ContextFold: 0.537 Pknots: 0.445 Positive Predictive Value ContextFold: 0.773 Pknots: 0.549 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.676 Pknots: 0.590 Sensitivity MXScarna(seed): 0.565 Pknots: 0.537 Positive Predictive Value MXScarna(seed): 0.815 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.668 Pknots: 0.514 Sensitivity RNAalifold(20): 0.519 Pknots: 0.467 Positive Predictive Value RNAalifold(20): 0.863 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Pknots: 0.381 Sensitivity PETfold_pre2.0(20): 0.530 Pknots: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.798 Pknots: 0.431 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.691 Pknots: 0.497 Sensitivity PPfold(20): 0.544 Pknots: 0.442 Positive Predictive Value PPfold(20): 0.881 Pknots: 0.565 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	52 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.654 Pknots: 0.515 Sensitivity IPknot: 0.552 Pknots: 0.464 Positive Predictive Value IPknot: 0.780 Pknots: 0.579 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.597 Pknots: 0.560 Sensitivity CentroidAlifold(seed): 0.398 Pknots: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.902 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.639 Pknots: 0.514 Sensitivity RNASampler(20): 0.488 Pknots: 0.467 Positive Predictive Value RNASampler(20): 0.842 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.655 Pknots: 0.497 Sensitivity TurboFold(20): 0.529 Pknots: 0.442 Positive Predictive Value TurboFold(20): 0.816 Pknots: 0.565 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	33 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.637 Pknots: 0.514 Sensitivity MXScarna(20): 0.530 Pknots: 0.467 Positive Predictive Value MXScarna(20): 0.769 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.673 Pknots: 0.601 Sensitivity Sfold: 0.579 Pknots: 0.545 Positive Predictive Value Sfold: 0.787 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.661 Pknots: 0.571 Sensitivity CentroidHomfold‑LAST: 0.538 Pknots: 0.506 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Pknots: 0.652 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.657 Pknots: 0.601 Sensitivity Contrafold: 0.585 Pknots: 0.545 Positive Predictive Value Contrafold: 0.743 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.633 Pknots: 0.595 Sensitivity RNAalifold(seed): 0.440 Pknots: 0.548 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.651 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.62644058675e-08	130 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.655 Pknots: 0.601 Sensitivity HotKnots: 0.588 Pknots: 0.545 Positive Predictive Value HotKnots: 0.735 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	110 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.659 Pknots: 0.598 Sensitivity MaxExpect: 0.584 Pknots: 0.544 Positive Predictive Value MaxExpect: 0.750 Pknots: 0.664 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	128 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.633 Pknots: 0.586 Sensitivity CentroidFold: 0.547 Pknots: 0.532 Positive Predictive Value CentroidFold: 0.739 Pknots: 0.652 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.661 Pknots: 0.601 Sensitivity UNAFold: 0.587 Pknots: 0.545 Positive Predictive Value UNAFold: 0.750 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.645 Pknots: 0.601 Sensitivity PknotsRG: 0.578 Pknots: 0.545 Positive Predictive Value PknotsRG: 0.726 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.656 Pknots: 0.598 Sensitivity ProbKnot: 0.595 Pknots: 0.542 Positive Predictive Value ProbKnot: 0.728 Pknots: 0.667 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.594 Pknots: 0.514 Sensitivity Murlet(20): 0.443 Pknots: 0.467 Positive Predictive Value Murlet(20): 0.801 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.650 Pknots: 0.601 Sensitivity RNAfold: 0.580 Pknots: 0.545 Positive Predictive Value RNAfold: 0.733 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.587 Pknots: 0.514 Sensitivity Carnac(20): 0.388 Pknots: 0.467 Positive Predictive Value Carnac(20): 0.894 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.645 Pknots: 0.601 Sensitivity RNAshapes: 0.573 Pknots: 0.545 Positive Predictive Value RNAshapes: 0.733 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	94 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.679 Pknots: 0.611 Sensitivity Fold: 0.612 Pknots: 0.554 Positive Predictive Value Fold: 0.758 Pknots: 0.680 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.544 Pknots: 0.450 Sensitivity TurboFold(seed): 0.439 Pknots: 0.407 Positive Predictive Value TurboFold(seed): 0.679 Pknots: 0.505 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	38 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.545 Pknots: 0.490 Sensitivity RSpredict(20): 0.424 Pknots: 0.447 Positive Predictive Value RSpredict(20): 0.707 Pknots: 0.544 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.662 Pknots: 0.639 Sensitivity Afold: 0.602 Pknots: 0.587 Positive Predictive Value Afold: 0.733 Pknots: 0.702 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.85233844192e-08	130 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.634 Pknots: 0.601 Sensitivity RNAsubopt: 0.568 Pknots: 0.545 Positive Predictive Value RNAsubopt: 0.713 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.537 Pknots: 0.491 Sensitivity RNASLOpt: 0.435 Pknots: 0.445 Positive Predictive Value RNASLOpt: 0.671 Pknots: 0.549 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.645 Cylofold: 0.637 Sensitivity Pknots: 0.578 Cylofold: 0.546 Positive Predictive Value Pknots: 0.726 Cylofold: 0.750 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.82713256396e-06	129 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.621 Pknots: 0.599 Sensitivity McQFold: 0.534 Pknots: 0.543 Positive Predictive Value McQFold: 0.729 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.561 Pknots: 0.532 Sensitivity Multilign(20): 0.466 Pknots: 0.468 Positive Predictive Value Multilign(20): 0.682 Pknots: 0.612 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39442331656e-08	32 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.585 Pknots: 0.545 Sensitivity CRWrnafold: 0.522 Pknots: 0.498 Positive Predictive Value CRWrnafold: 0.663 Pknots: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.635 RNASampler(seed): 0.635 Sensitivity Pknots: 0.608 RNASampler(seed): 0.484 Positive Predictive Value Pknots: 0.669 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.499189968383	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.705 Alterna: 0.665 Sensitivity Pknots: 0.633 Alterna: 0.599 Positive Predictive Value Pknots: 0.791 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.542 Pknots: 0.514 Sensitivity Mastr(20): 0.378 Pknots: 0.467 Positive Predictive Value Mastr(20): 0.784 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 2.45033651981e-07	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.625 Vsfold4: 0.581 Sensitivity Pknots: 0.564 Vsfold4: 0.493 Positive Predictive Value Pknots: 0.698 Vsfold4: 0.692 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.588 Murlet(seed): 0.514 Sensitivity Pknots: 0.542 Murlet(seed): 0.315 Positive Predictive Value Pknots: 0.644 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.628 Vsfold5: 0.542 Sensitivity Pknots: 0.567 Vsfold5: 0.469 Positive Predictive Value Pknots: 0.703 Vsfold5: 0.634 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.588 MCFold: 0.522 Sensitivity Pknots: 0.535 MCFold: 0.535 Positive Predictive Value Pknots: 0.652 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.698 RDfolder: 0.592 Sensitivity Pknots: 0.628 RDfolder: 0.491 Positive Predictive Value Pknots: 0.783 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.506 RNAwolf: 0.427 Sensitivity Pknots: 0.456 RNAwolf: 0.401 Positive Predictive Value Pknots: 0.570 RNAwolf: 0.463 Number of pairs reference - predicted secondary structure: 64 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.546 Pknots: 0.519 Sensitivity CMfinder(20): 0.366 Pknots: 0.439 Positive Predictive Value CMfinder(20): 0.822 Pknots: 0.621 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.517 NanoFolder: 0.376 Sensitivity Pknots: 0.463 NanoFolder: 0.386 Positive Predictive Value Pknots: 0.584 NanoFolder: 0.377 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.558 Pknots: 0.494 Sensitivity Multilign(seed): 0.434 Pknots: 0.441 Positive Predictive Value Multilign(seed): 0.725 Pknots: 0.563 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.511 PPfold(seed): 0.092 Sensitivity Pknots: 0.449 PPfold(seed): 0.016 Positive Predictive Value Pknots: 0.589 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.567 RSpredict(seed): 0.276 Sensitivity Pknots: 0.516 RSpredict(seed): 0.134 Positive Predictive Value Pknots: 0.629 RSpredict(seed): 0.576 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.578 Carnac(seed): 0.241 Sensitivity Pknots: 0.532 Carnac(seed): 0.058 Positive Predictive Value Pknots: 0.634 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.580 Mastr(seed): 0.251 Sensitivity Pknots: 0.526 Mastr(seed): 0.071 Positive Predictive Value Pknots: 0.645 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Pknots: 0.607 Sensitivity PETfold_2.0(seed): 0.642 Pknots: 0.516 Positive Predictive Value PETfold_2.0(seed): 0.924 Pknots: 0.721 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Pknots: 0.410 Sensitivity PETfold_2.0(20): 0.509 Pknots: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 Pknots: 0.514 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASampler(seed)	10 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.502 RNASampler(seed): 0.473 Sensitivity CentroidAlifold(20): 0.332 RNASampler(seed): 0.347 Positive Predictive Value CentroidAlifold(20): 0.763 RNASampler(seed): 0.651 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.14531876181e-08	7 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.594 RNASampler(seed): 0.333 Sensitivity PETfold_pre2.0(seed): 0.453 RNASampler(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.782 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.478 RNASampler(seed): 0.317 Sensitivity ContextFold: 0.386 RNASampler(seed): 0.207 Positive Predictive Value ContextFold: 0.596 RNASampler(seed): 0.492 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	19 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 RNASampler(seed): 0.635 Sensitivity MXScarna(seed): 0.532 RNASampler(seed): 0.484 Positive Predictive Value MXScarna(seed): 0.789 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	9 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 RNAalifold(20): 0.493 Sensitivity RNASampler(seed): 0.399 RNAalifold(20): 0.385 Positive Predictive Value RNASampler(seed): 0.739 RNAalifold(20): 0.636 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.299 PETfold_pre2.0(20): 0.262 Sensitivity RNASampler(seed): 0.214 PETfold_pre2.0(20): 0.195 Positive Predictive Value RNASampler(seed): 0.423 PETfold_pre2.0(20): 0.357 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.513 PPfold(20): 0.507 Sensitivity RNASampler(seed): 0.359 PPfold(20): 0.365 Positive Predictive Value RNASampler(seed): 0.739 PPfold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.547 RNASampler(seed): 0.447 Sensitivity IPknot: 0.416 RNASampler(seed): 0.299 Positive Predictive Value IPknot: 0.724 RNASampler(seed): 0.673 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	21 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.639 RNASampler(seed): 0.586 Sensitivity CentroidAlifold(seed): 0.476 RNASampler(seed): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.862 RNASampler(seed): 0.787 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	9 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 RNASampler(20): 0.528 Sensitivity RNASampler(seed): 0.399 RNASampler(20): 0.426 Positive Predictive Value RNASampler(seed): 0.739 RNASampler(20): 0.660 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.532 RNASampler(seed): 0.513 Sensitivity TurboFold(20): 0.425 RNASampler(seed): 0.359 Positive Predictive Value TurboFold(20): 0.670 RNASampler(seed): 0.739 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 MXScarna(20): 0.519 Sensitivity RNASampler(seed): 0.399 MXScarna(20): 0.423 Positive Predictive Value RNASampler(seed): 0.739 MXScarna(20): 0.641 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.678 RNASampler(seed): 0.635 Sensitivity Sfold: 0.588 RNASampler(seed): 0.484 Positive Predictive Value Sfold: 0.785 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	6 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.574 RNASampler(seed): 0.509 Sensitivity CentroidHomfold‑LAST: 0.471 RNASampler(seed): 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.706 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	19 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.671 RNASampler(seed): 0.635 Sensitivity Contrafold: 0.603 RNASampler(seed): 0.484 Positive Predictive Value Contrafold: 0.751 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.34821445183e-08	19 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 RNAalifold(seed): 0.629 Sensitivity RNASampler(seed): 0.484 RNAalifold(seed): 0.451 Positive Predictive Value RNASampler(seed): 0.837 RNAalifold(seed): 0.881 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30966813656e-06	19 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.635 HotKnots: 0.620 Sensitivity RNASampler(seed): 0.484 HotKnots: 0.579 Positive Predictive Value RNASampler(seed): 0.837 HotKnots: 0.669 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.31679015848e-06	17 MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.644 RNASampler(seed): 0.623 Sensitivity MaxExpect: 0.578 RNASampler(seed): 0.475 Positive Predictive Value MaxExpect: 0.722 RNASampler(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.54671126599e-08	21 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.647 RNASampler(seed): 0.586 Sensitivity CentroidFold: 0.556 RNASampler(seed): 0.440 Positive Predictive Value CentroidFold: 0.758 RNASampler(seed): 0.787 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	19 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.639 RNASampler(seed): 0.635 Sensitivity UNAFold: 0.584 RNASampler(seed): 0.484 Positive Predictive Value UNAFold: 0.704 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7981009876e-07	19 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.639 RNASampler(seed): 0.635 Sensitivity PknotsRG: 0.588 RNASampler(seed): 0.484 Positive Predictive Value PknotsRG: 0.699 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000481443120598	10 ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.560 RNASampler(seed): 0.528 Sensitivity ProbKnot: 0.526 RNASampler(seed): 0.375 Positive Predictive Value ProbKnot: 0.602 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.63443860185e-08	9 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Murlet(20): 0.470 Sensitivity RNASampler(seed): 0.399 Murlet(20): 0.357 Positive Predictive Value RNASampler(seed): 0.739 Murlet(20): 0.623 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.657 RNASampler(seed): 0.635 Sensitivity RNAfold: 0.604 RNASampler(seed): 0.484 Positive Predictive Value RNAfold: 0.719 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	9 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Carnac(20): 0.534 Sensitivity RNASampler(seed): 0.399 Carnac(20): 0.306 Positive Predictive Value RNASampler(seed): 0.739 Carnac(20): 0.937 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.640 RNASampler(seed): 0.635 Sensitivity RNAshapes: 0.588 RNASampler(seed): 0.484 Positive Predictive Value RNAshapes: 0.702 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 7.17916828225e-08	14 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.614 Fold: 0.608 Sensitivity RNASampler(seed): 0.461 Fold: 0.571 Positive Predictive Value RNASampler(seed): 0.822 Fold: 0.654 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00454636894862	6 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.461 TurboFold(seed): 0.458 Sensitivity RNASampler(seed): 0.323 TurboFold(seed): 0.383 Positive Predictive Value RNASampler(seed): 0.663 TurboFold(seed): 0.554 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	11 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.492 RSpredict(20): 0.423 Sensitivity RNASampler(seed): 0.364 RSpredict(20): 0.369 Positive Predictive Value RNASampler(seed): 0.668 RSpredict(20): 0.489 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.29018360962e-08	17 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.695 RNASampler(seed): 0.669 Sensitivity Afold: 0.649 RNASampler(seed): 0.528 Positive Predictive Value Afold: 0.749 RNASampler(seed): 0.852 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	19 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.635 RNAsubopt: 0.616 Sensitivity RNASampler(seed): 0.484 RNAsubopt: 0.571 Positive Predictive Value RNASampler(seed): 0.837 RNAsubopt: 0.670 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.41690547646e-08	4 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.425 RNASampler(seed): 0.317 Sensitivity RNASLOpt: 0.372 RNASampler(seed): 0.207 Positive Predictive Value RNASLOpt: 0.491 RNASampler(seed): 0.492 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.659 RNASampler(seed): 0.601 Sensitivity Cylofold: 0.579 RNASampler(seed): 0.433 Positive Predictive Value Cylofold: 0.755 RNASampler(seed): 0.839 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.635 McQFold: 0.628 Sensitivity RNASampler(seed): 0.484 McQFold: 0.562 Positive Predictive Value RNASampler(seed): 0.837 McQFold: 0.707 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.0398923262603	4 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.581 Multilign(20): 0.559 Sensitivity RNASampler(seed): 0.426 Multilign(20): 0.504 Positive Predictive Value RNASampler(seed): 0.797 Multilign(20): 0.625 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.357 CRWrnafold: 0.262 Sensitivity RNASampler(seed): 0.253 CRWrnafold: 0.253 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.279 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	19 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.635 RNASampler(seed): 0.635 Sensitivity Pknots: 0.608 RNASampler(seed): 0.484 Positive Predictive Value Pknots: 0.669 RNASampler(seed): 0.837 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.499189968383		- Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.807 RNASampler(seed): 0.753 Sensitivity Alterna: 0.727 RNASampler(seed): 0.603 Positive Predictive Value Alterna: 0.900 RNASampler(seed): 0.946 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	? RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Mastr(20): 0.510 Sensitivity RNASampler(seed): 0.399 Mastr(20): 0.289 Positive Predictive Value RNASampler(seed): 0.739 Mastr(20): 0.903 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.663 Vsfold4: 0.602 Sensitivity RNASampler(seed): 0.515 Vsfold4: 0.526 Positive Predictive Value RNASampler(seed): 0.857 Vsfold4: 0.695 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 7.21563533328e-09	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Murlet(seed): 0.538 Sensitivity RNASampler(seed): 0.484 Murlet(seed): 0.349 Positive Predictive Value RNASampler(seed): 0.837 Murlet(seed): 0.833 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.663 Vsfold5: 0.632 Sensitivity RNASampler(seed): 0.515 Vsfold5: 0.571 Positive Predictive Value RNASampler(seed): 0.857 Vsfold5: 0.706 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.88234616094e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.598 MCFold: 0.512 Sensitivity RNASampler(seed): 0.458 MCFold: 0.532 Positive Predictive Value RNASampler(seed): 0.786 MCFold: 0.498 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.734 RDfolder: 0.632 Sensitivity RNASampler(seed): 0.572 RDfolder: 0.518 Positive Predictive Value RNASampler(seed): 0.949 RDfolder: 0.779 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.417 RNAwolf: 0.340 Sensitivity RNASampler(seed): 0.283 RNAwolf: 0.333 Positive Predictive Value RNASampler(seed): 0.619 RNAwolf: 0.353 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.318 NanoFolder: 0.169 Sensitivity RNASampler(seed): 0.215 NanoFolder: 0.194 Positive Predictive Value RNASampler(seed): 0.476 NanoFolder: 0.157 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.597 RNASampler(seed): 0.502 Sensitivity Multilign(seed): 0.476 RNASampler(seed): 0.332 Positive Predictive Value Multilign(seed): 0.756 RNASampler(seed): 0.767 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.447 PPfold(seed): 0.160 Sensitivity RNASampler(seed): 0.299 PPfold(seed): 0.050 Positive Predictive Value RNASampler(seed): 0.673 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.594 RSpredict(seed): 0.467 Sensitivity RNASampler(seed): 0.448 RSpredict(seed): 0.298 Positive Predictive Value RNASampler(seed): 0.793 RSpredict(seed): 0.737 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Carnac(seed): 0.346 Sensitivity RNASampler(seed): 0.484 Carnac(seed): 0.120 Positive Predictive Value RNASampler(seed): 0.837 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Mastr(seed): 0.440 Sensitivity RNASampler(seed): 0.484 Mastr(seed): 0.216 Positive Predictive Value RNASampler(seed): 0.837 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	? RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Alterna	12 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.750 Alterna: 0.558 Sensitivity CentroidAlifold(20): 0.608 Alterna: 0.491 Positive Predictive Value CentroidAlifold(20): 0.930 Alterna: 0.643 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	3 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Alterna: 0.545 Sensitivity PETfold_pre2.0(seed): 0.540 Alterna: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.690 Alterna: 0.601 Sensitivity ContextFold: 0.587 Alterna: 0.537 Positive Predictive Value ContextFold: 0.819 Alterna: 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	29 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.725 Alterna: 0.655 Sensitivity MXScarna(seed): 0.609 Alterna: 0.587 Positive Predictive Value MXScarna(seed): 0.869 Alterna: 0.737 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	13 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.729 Alterna: 0.571 Sensitivity RNAalifold(20): 0.590 Alterna: 0.504 Positive Predictive Value RNAalifold(20): 0.907 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.00475527001e-08	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.726 Alterna: 0.654 Sensitivity PPfold(20): 0.569 Alterna: 0.569 Positive Predictive Value PPfold(20): 0.933 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	22 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.683 Alterna: 0.589 Sensitivity IPknot: 0.568 Alterna: 0.527 Positive Predictive Value IPknot: 0.829 Alterna: 0.669 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.650 CentroidAlifold(seed): 0.592 Sensitivity Alterna: 0.583 CentroidAlifold(seed): 0.415 Positive Predictive Value Alterna: 0.733 CentroidAlifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.767 Alterna: 0.571 Sensitivity RNASampler(20): 0.620 Alterna: 0.504 Positive Predictive Value RNASampler(20): 0.953 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.22797000563e-08	4 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.721 Alterna: 0.654 Sensitivity TurboFold(20): 0.602 Alterna: 0.569 Positive Predictive Value TurboFold(20): 0.871 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	13 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.724 Alterna: 0.571 Sensitivity MXScarna(20): 0.601 Alterna: 0.504 Positive Predictive Value MXScarna(20): 0.879 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	89 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.719 Alterna: 0.665 Sensitivity Sfold: 0.625 Alterna: 0.599 Positive Predictive Value Sfold: 0.833 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Alterna: 0.608 Sensitivity CentroidHomfold‑LAST: 0.533 Alterna: 0.544 Positive Predictive Value CentroidHomfold‑LAST: 0.915 Alterna: 0.690 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	89 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.730 Alterna: 0.665 Sensitivity Contrafold: 0.648 Alterna: 0.599 Positive Predictive Value Contrafold: 0.829 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.763 RNAalifold(seed): 0.672 Sensitivity Alterna: 0.683 RNAalifold(seed): 0.524 Positive Predictive Value Alterna: 0.858 RNAalifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	89 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.719 Alterna: 0.665 Sensitivity HotKnots: 0.645 Alterna: 0.599 Positive Predictive Value HotKnots: 0.808 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	70 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.713 Alterna: 0.654 Sensitivity MaxExpect: 0.636 Alterna: 0.593 Positive Predictive Value MaxExpect: 0.805 Alterna: 0.729 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	76 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.738 Alterna: 0.651 Sensitivity CentroidFold: 0.643 Alterna: 0.590 Positive Predictive Value CentroidFold: 0.853 Alterna: 0.728 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.722 Alterna: 0.665 Sensitivity UNAFold: 0.642 Alterna: 0.599 Positive Predictive Value UNAFold: 0.819 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.699 Alterna: 0.665 Sensitivity PknotsRG: 0.625 Alterna: 0.599 Positive Predictive Value PknotsRG: 0.789 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.723 Alterna: 0.688 Sensitivity ProbKnot: 0.671 Alterna: 0.630 Positive Predictive Value ProbKnot: 0.785 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.658 Alterna: 0.571 Sensitivity Murlet(20): 0.510 Alterna: 0.504 Positive Predictive Value Murlet(20): 0.856 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	89 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.709 Alterna: 0.665 Sensitivity RNAfold: 0.633 Alterna: 0.599 Positive Predictive Value RNAfold: 0.801 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.662 Alterna: 0.571 Sensitivity Carnac(20): 0.477 Alterna: 0.504 Positive Predictive Value Carnac(20): 0.925 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	89 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.698 Alterna: 0.665 Sensitivity RNAshapes: 0.618 Alterna: 0.599 Positive Predictive Value RNAshapes: 0.796 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.751 Alterna: 0.698 Sensitivity Fold: 0.684 Alterna: 0.640 Positive Predictive Value Fold: 0.832 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.624 TurboFold(seed): 0.594 Sensitivity Alterna: 0.534 TurboFold(seed): 0.500 Positive Predictive Value Alterna: 0.738 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	13 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.667 Alterna: 0.571 Sensitivity RSpredict(20): 0.526 Alterna: 0.504 Positive Predictive Value RSpredict(20): 0.853 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	69 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.710 Alterna: 0.683 Sensitivity Afold: 0.647 Alterna: 0.618 Positive Predictive Value Afold: 0.788 Alterna: 0.763 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.692 Alterna: 0.665 Sensitivity RNAsubopt: 0.616 Alterna: 0.599 Positive Predictive Value RNAsubopt: 0.786 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.601 RNASLOpt: 0.567 Sensitivity Alterna: 0.537 RNASLOpt: 0.458 Positive Predictive Value Alterna: 0.684 RNASLOpt: 0.713 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	45 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.700 Alterna: 0.671 Sensitivity Cylofold: 0.608 Alterna: 0.613 Positive Predictive Value Cylofold: 0.813 Alterna: 0.743 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.700 Alterna: 0.665 Sensitivity McQFold: 0.600 Alterna: 0.599 Positive Predictive Value McQFold: 0.826 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.706 Alterna: 0.654 Sensitivity Multilign(20): 0.610 Alterna: 0.569 Positive Predictive Value Multilign(20): 0.824 Alterna: 0.761 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	19 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.593 Alterna: 0.586 Sensitivity CRWrnafold: 0.535 Alterna: 0.535 Positive Predictive Value CRWrnafold: 0.668 Alterna: 0.654 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000144846895958	89 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.705 Alterna: 0.665 Sensitivity Pknots: 0.633 Alterna: 0.599 Positive Predictive Value Pknots: 0.791 Alterna: 0.748 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.807 RNASampler(seed): 0.753 Sensitivity Alterna: 0.727 RNASampler(seed): 0.603 Positive Predictive Value Alterna: 0.900 RNASampler(seed): 0.946 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08		- Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.699 Alterna: 0.571 Sensitivity Mastr(20): 0.562 Alterna: 0.504 Positive Predictive Value Mastr(20): 0.876 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.665 Vsfold4: 0.655 Sensitivity Alterna: 0.599 Vsfold4: 0.559 Positive Predictive Value Alterna: 0.748 Vsfold4: 0.775 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 1.37177523642e-07	+ Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.758 Murlet(seed): 0.594 Sensitivity Alterna: 0.676 Murlet(seed): 0.425 Positive Predictive Value Alterna: 0.854 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.665 Vsfold5: 0.623 Sensitivity Alterna: 0.599 Vsfold5: 0.542 Positive Predictive Value Alterna: 0.748 Vsfold5: 0.725 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.681 MCFold: 0.606 Sensitivity Alterna: 0.614 MCFold: 0.624 Positive Predictive Value Alterna: 0.764 MCFold: 0.599 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.668 RDfolder: 0.602 Sensitivity Alterna: 0.602 RDfolder: 0.502 Positive Predictive Value Alterna: 0.750 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.589 RNAwolf: 0.584 Sensitivity Alterna: 0.527 RNAwolf: 0.543 Positive Predictive Value Alterna: 0.669 RNAwolf: 0.639 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00321277492933	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.654 NanoFolder: 0.539 Sensitivity Alterna: 0.567 NanoFolder: 0.533 Positive Predictive Value Alterna: 0.764 NanoFolder: 0.557 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.624 Multilign(seed): 0.588 Sensitivity Alterna: 0.534 Multilign(seed): 0.483 Positive Predictive Value Alterna: 0.738 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.566 PPfold(seed): 0.153 Sensitivity Alterna: 0.479 PPfold(seed): 0.032 Positive Predictive Value Alterna: 0.679 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.655 RSpredict(seed): 0.435 Sensitivity Alterna: 0.587 RSpredict(seed): 0.264 Positive Predictive Value Alterna: 0.737 RSpredict(seed): 0.729 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.758 Carnac(seed): 0.382 Sensitivity Alterna: 0.676 Carnac(seed): 0.147 Positive Predictive Value Alterna: 0.854 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.655 Mastr(seed): 0.367 Sensitivity Alterna: 0.587 Mastr(seed): 0.151 Positive Predictive Value Alterna: 0.737 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(20)	39 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Mastr(20): 0.499 Sensitivity CentroidAlifold(20): 0.516 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(20): 0.879 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(seed): 0.597 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.20167918023e-08	11 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.660 Mastr(20): 0.475 Sensitivity ContextFold: 0.525 Mastr(20): 0.308 Positive Predictive Value ContextFold: 0.835 Mastr(20): 0.740 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.93000771886e-09	33 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.659 Mastr(20): 0.516 Sensitivity MXScarna(seed): 0.545 Mastr(20): 0.341 Positive Predictive Value MXScarna(seed): 0.801 Mastr(20): 0.786 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(20): 0.514 Sensitivity RNAalifold(20): 0.502 Mastr(20): 0.339 Positive Predictive Value RNAalifold(20): 0.860 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	15 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.691 Mastr(20): 0.537 Sensitivity PPfold(20): 0.544 Mastr(20): 0.369 Positive Predictive Value PPfold(20): 0.881 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	14 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.601 Mastr(20): 0.521 Sensitivity IPknot: 0.485 Mastr(20): 0.352 Positive Predictive Value IPknot: 0.751 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49381627234e-08	39 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.589 Mastr(20): 0.499 Sensitivity CentroidAlifold(seed): 0.379 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.920 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.623 Mastr(20): 0.514 Sensitivity RNASampler(20): 0.470 Mastr(20): 0.339 Positive Predictive Value RNASampler(20): 0.830 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.655 Mastr(20): 0.537 Sensitivity TurboFold(20): 0.529 Mastr(20): 0.369 Positive Predictive Value TurboFold(20): 0.816 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	34 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.624 Mastr(20): 0.514 Sensitivity MXScarna(20): 0.518 Mastr(20): 0.339 Positive Predictive Value MXScarna(20): 0.756 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.587 Mastr(20): 0.514 Sensitivity Sfold: 0.490 Mastr(20): 0.339 Positive Predictive Value Sfold: 0.708 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Mastr(20): 0.566 Sensitivity CentroidHomfold‑LAST: 0.549 Mastr(20): 0.409 Positive Predictive Value CentroidHomfold‑LAST: 0.764 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	34 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.551 Mastr(20): 0.514 Sensitivity Contrafold: 0.486 Mastr(20): 0.339 Positive Predictive Value Contrafold: 0.630 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	20 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.570 Mastr(20): 0.393 Sensitivity RNAalifold(seed): 0.351 Mastr(20): 0.198 Positive Predictive Value RNAalifold(seed): 0.930 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	34 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.556 Mastr(20): 0.514 Sensitivity HotKnots: 0.495 Mastr(20): 0.339 Positive Predictive Value HotKnots: 0.628 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.580 Mastr(20): 0.511 Sensitivity MaxExpect: 0.503 Mastr(20): 0.335 Positive Predictive Value MaxExpect: 0.674 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.537 Mastr(20): 0.499 Sensitivity CentroidFold: 0.456 Mastr(20): 0.333 Positive Predictive Value CentroidFold: 0.637 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.572 Mastr(20): 0.514 Sensitivity UNAFold: 0.501 Mastr(20): 0.339 Positive Predictive Value UNAFold: 0.658 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.572 Mastr(20): 0.514 Sensitivity PknotsRG: 0.508 Mastr(20): 0.339 Positive Predictive Value PknotsRG: 0.647 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.578 Mastr(20): 0.485 Sensitivity ProbKnot: 0.516 Mastr(20): 0.303 Positive Predictive Value ProbKnot: 0.653 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	34 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.577 Mastr(20): 0.514 Sensitivity Murlet(20): 0.423 Mastr(20): 0.339 Positive Predictive Value Murlet(20): 0.791 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.562 Mastr(20): 0.514 Sensitivity RNAfold: 0.497 Mastr(20): 0.339 Positive Predictive Value RNAfold: 0.640 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	34 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.577 Mastr(20): 0.514 Sensitivity Carnac(20): 0.372 Mastr(20): 0.339 Positive Predictive Value Carnac(20): 0.897 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.567 Mastr(20): 0.514 Sensitivity RNAshapes: 0.498 Mastr(20): 0.339 Positive Predictive Value RNAshapes: 0.651 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.589 Mastr(20): 0.485 Sensitivity Fold: 0.525 Mastr(20): 0.303 Positive Predictive Value Fold: 0.664 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.565 Mastr(20): 0.523 Sensitivity TurboFold(seed): 0.454 Mastr(20): 0.333 Positive Predictive Value TurboFold(seed): 0.708 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	39 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.544 Mastr(20): 0.515 Sensitivity RSpredict(20): 0.425 Mastr(20): 0.345 Positive Predictive Value RSpredict(20): 0.701 Mastr(20): 0.773 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.544 Afold: 0.530 Sensitivity Mastr(20): 0.367 Afold: 0.478 Positive Predictive Value Mastr(20): 0.811 Afold: 0.591 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.4733335145e-06	34 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.549 Mastr(20): 0.514 Sensitivity RNAsubopt: 0.490 Mastr(20): 0.339 Positive Predictive Value RNAsubopt: 0.620 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.53888633552e-08	11 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.540 Mastr(20): 0.475 Sensitivity RNASLOpt: 0.443 Mastr(20): 0.308 Positive Predictive Value RNASLOpt: 0.664 Mastr(20): 0.740 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	19 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.616 Mastr(20): 0.553 Sensitivity Cylofold: 0.528 Mastr(20): 0.381 Positive Predictive Value Cylofold: 0.725 Mastr(20): 0.809 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	34 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.539 Mastr(20): 0.514 Sensitivity McQFold: 0.462 Mastr(20): 0.339 Positive Predictive Value McQFold: 0.633 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.53888633552e-08	15 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.561 Mastr(20): 0.554 Sensitivity Multilign(20): 0.466 Mastr(20): 0.389 Positive Predictive Value Multilign(20): 0.682 Mastr(20): 0.795 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000912413615127	7 Mastr(20) vs CRWrnafold Matthews Correlation Coefficient Mastr(20): 0.547 CRWrnafold: 0.546 Sensitivity Mastr(20): 0.373 CRWrnafold: 0.483 Positive Predictive Value Mastr(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	33 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.542 Pknots: 0.514 Sensitivity Mastr(20): 0.378 Pknots: 0.467 Positive Predictive Value Mastr(20): 0.784 Pknots: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 2.45033651981e-07	9 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.541 Mastr(20): 0.510 Sensitivity RNASampler(seed): 0.399 Mastr(20): 0.289 Positive Predictive Value RNASampler(seed): 0.739 Mastr(20): 0.903 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	13 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.699 Alterna: 0.571 Sensitivity Mastr(20): 0.562 Alterna: 0.504 Positive Predictive Value Mastr(20): 0.876 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08		+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold4: 0.477 Sensitivity Mastr(20): 0.354 Vsfold4: 0.401 Positive Predictive Value Mastr(20): 0.784 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.463 Mastr(20): 0.430 Sensitivity Murlet(seed): 0.250 Mastr(20): 0.237 Positive Predictive Value Murlet(seed): 0.863 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold5: 0.417 Sensitivity Mastr(20): 0.354 Vsfold5: 0.355 Positive Predictive Value Mastr(20): 0.784 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.562 MCFold: 0.401 Sensitivity Mastr(20): 0.391 MCFold: 0.418 Positive Predictive Value Mastr(20): 0.811 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.667 RDfolder: 0.541 Sensitivity Mastr(20): 0.516 RDfolder: 0.440 Positive Predictive Value Mastr(20): 0.868 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.496 RNAwolf: 0.348 Sensitivity Mastr(20): 0.341 RNAwolf: 0.328 Positive Predictive Value Mastr(20): 0.729 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): 0.575 CMfinder(20): 0.546 Sensitivity Mastr(20): 0.421 CMfinder(20): 0.366 Positive Predictive Value Mastr(20): 0.793 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.505 NanoFolder: 0.276 Sensitivity Mastr(20): 0.370 NanoFolder: 0.286 Positive Predictive Value Mastr(20): 0.697 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Mastr(20): 0.522 Sensitivity Multilign(seed): 0.468 Mastr(20): 0.342 Positive Predictive Value Multilign(seed): 0.795 Mastr(20): 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.521 PPfold(seed): 0.061 Sensitivity Mastr(20): 0.352 PPfold(seed): 0.010 Positive Predictive Value Mastr(20): 0.778 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.515 RSpredict(seed): 0.191 Sensitivity Mastr(20): 0.345 RSpredict(seed): 0.079 Positive Predictive Value Mastr(20): 0.773 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.498 Carnac(seed): 0.186 Sensitivity Mastr(20): 0.320 Carnac(seed): 0.035 Positive Predictive Value Mastr(20): 0.780 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.514 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.339 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.784 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Mastr(20): 0.189 Sensitivity PETfold_2.0(seed): 0.614 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(20): 0.189 Sensitivity PETfold_2.0(20): 0.509 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Vsfold4	38 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.681 Vsfold4: 0.445 Sensitivity CentroidAlifold(20): 0.527 Vsfold4: 0.373 Positive Predictive Value CentroidAlifold(20): 0.882 Vsfold4: 0.536 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.452 Sensitivity PETfold_pre2.0(seed): 0.605 Vsfold4: 0.371 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	41 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.660 Vsfold4: 0.500 Sensitivity ContextFold: 0.549 Vsfold4: 0.418 Positive Predictive Value ContextFold: 0.797 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.675 Vsfold4: 0.532 Sensitivity MXScarna(seed): 0.566 Vsfold4: 0.456 Positive Predictive Value MXScarna(seed): 0.810 Vsfold4: 0.624 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.666 Vsfold4: 0.477 Sensitivity RNAalifold(20): 0.512 Vsfold4: 0.401 Positive Predictive Value RNAalifold(20): 0.870 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold4: 0.421 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold4: 0.346 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	14 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.723 Vsfold4: 0.535 Sensitivity PPfold(20): 0.581 Vsfold4: 0.442 Positive Predictive Value PPfold(20): 0.905 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	49 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.650 Vsfold4: 0.505 Sensitivity IPknot: 0.554 Vsfold4: 0.424 Positive Predictive Value IPknot: 0.769 Vsfold4: 0.610 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold4: 0.499 Sensitivity CentroidAlifold(seed): 0.393 Vsfold4: 0.425 Positive Predictive Value CentroidAlifold(seed): 0.887 Vsfold4: 0.591 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.637 Vsfold4: 0.477 Sensitivity RNASampler(20): 0.482 Vsfold4: 0.401 Positive Predictive Value RNASampler(20): 0.846 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.681 Vsfold4: 0.535 Sensitivity TurboFold(20): 0.558 Vsfold4: 0.442 Positive Predictive Value TurboFold(20): 0.836 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	33 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.635 Vsfold4: 0.477 Sensitivity MXScarna(20): 0.531 Vsfold4: 0.401 Positive Predictive Value MXScarna(20): 0.764 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.652 Vsfold4: 0.547 Sensitivity Sfold: 0.564 Vsfold4: 0.465 Positive Predictive Value Sfold: 0.759 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.624 Vsfold4: 0.516 Sensitivity CentroidHomfold‑LAST: 0.484 Vsfold4: 0.430 Positive Predictive Value CentroidHomfold‑LAST: 0.811 Vsfold4: 0.626 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.642 Vsfold4: 0.547 Sensitivity Contrafold: 0.574 Vsfold4: 0.465 Positive Predictive Value Contrafold: 0.722 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.600 Vsfold4: 0.506 Sensitivity RNAalifold(seed): 0.403 Vsfold4: 0.439 Positive Predictive Value RNAalifold(seed): 0.895 Vsfold4: 0.589 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.642 Vsfold4: 0.547 Sensitivity HotKnots: 0.578 Vsfold4: 0.465 Positive Predictive Value HotKnots: 0.718 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.638 Vsfold4: 0.543 Sensitivity MaxExpect: 0.568 Vsfold4: 0.462 Positive Predictive Value MaxExpect: 0.720 Vsfold4: 0.643 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.625 Vsfold4: 0.524 Sensitivity CentroidFold: 0.543 Vsfold4: 0.445 Positive Predictive Value CentroidFold: 0.723 Vsfold4: 0.624 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.643 Vsfold4: 0.547 Sensitivity UNAFold: 0.573 Vsfold4: 0.465 Positive Predictive Value UNAFold: 0.726 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.628 Vsfold4: 0.547 Sensitivity PknotsRG: 0.565 Vsfold4: 0.465 Positive Predictive Value PknotsRG: 0.703 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	85 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.628 Vsfold4: 0.528 Sensitivity ProbKnot: 0.575 Vsfold4: 0.450 Positive Predictive Value ProbKnot: 0.691 Vsfold4: 0.625 Number of pairs reference - predicted secondary structure: 85 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.586 Vsfold4: 0.477 Sensitivity Murlet(20): 0.431 Vsfold4: 0.401 Positive Predictive Value Murlet(20): 0.801 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.633 Vsfold4: 0.547 Sensitivity RNAfold: 0.568 Vsfold4: 0.465 Positive Predictive Value RNAfold: 0.711 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.585 Vsfold4: 0.477 Sensitivity Carnac(20): 0.382 Vsfold4: 0.401 Positive Predictive Value Carnac(20): 0.900 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.624 Vsfold4: 0.547 Sensitivity RNAshapes: 0.555 Vsfold4: 0.465 Positive Predictive Value RNAshapes: 0.706 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.656 Vsfold4: 0.550 Sensitivity Fold: 0.594 Vsfold4: 0.470 Positive Predictive Value Fold: 0.730 Vsfold4: 0.648 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.550 Vsfold4: 0.423 Sensitivity TurboFold(seed): 0.456 Vsfold4: 0.346 Positive Predictive Value TurboFold(seed): 0.672 Vsfold4: 0.527 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	38 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.554 Vsfold4: 0.459 Sensitivity RSpredict(20): 0.433 Vsfold4: 0.387 Positive Predictive Value RSpredict(20): 0.713 Vsfold4: 0.549 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.625 Vsfold4: 0.553 Sensitivity Afold: 0.571 Vsfold4: 0.474 Positive Predictive Value Afold: 0.689 Vsfold4: 0.652 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.618 Vsfold4: 0.547 Sensitivity RNAsubopt: 0.557 Vsfold4: 0.465 Positive Predictive Value RNAsubopt: 0.691 Vsfold4: 0.650 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.552 Vsfold4: 0.500 Sensitivity RNASLOpt: 0.447 Vsfold4: 0.418 Positive Predictive Value RNASLOpt: 0.688 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.612 Vsfold4: 0.563 Sensitivity Cylofold: 0.524 Vsfold4: 0.477 Positive Predictive Value Cylofold: 0.722 Vsfold4: 0.673 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	128 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.599 Vsfold4: 0.545 Sensitivity McQFold: 0.519 Vsfold4: 0.463 Positive Predictive Value McQFold: 0.696 Vsfold4: 0.648 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.561 Vsfold4: 0.490 Sensitivity Multilign(20): 0.466 Vsfold4: 0.407 Positive Predictive Value Multilign(20): 0.682 Vsfold4: 0.599 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	32 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.585 Vsfold4: 0.502 Sensitivity CRWrnafold: 0.522 Vsfold4: 0.431 Positive Predictive Value CRWrnafold: 0.663 Vsfold4: 0.595 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	125 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.625 Vsfold4: 0.581 Sensitivity Pknots: 0.564 Vsfold4: 0.493 Positive Predictive Value Pknots: 0.698 Vsfold4: 0.692 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.663 Vsfold4: 0.602 Sensitivity RNASampler(seed): 0.515 Vsfold4: 0.526 Positive Predictive Value RNASampler(seed): 0.857 Vsfold4: 0.695 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 7.21563533328e-09	89 Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.665 Vsfold4: 0.655 Sensitivity Alterna: 0.599 Vsfold4: 0.559 Positive Predictive Value Alterna: 0.748 Vsfold4: 0.775 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 1.37177523642e-07	33 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold4: 0.477 Sensitivity Mastr(20): 0.354 Vsfold4: 0.401 Positive Predictive Value Mastr(20): 0.784 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.546 Murlet(seed): 0.519 Sensitivity Vsfold4: 0.465 Murlet(seed): 0.323 Positive Predictive Value Vsfold4: 0.648 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.550 Vsfold5: 0.514 Sensitivity Vsfold4: 0.468 Vsfold5: 0.445 Positive Predictive Value Vsfold4: 0.653 Vsfold5: 0.600 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.562 MCFold: 0.539 Sensitivity Vsfold4: 0.477 MCFold: 0.552 Positive Predictive Value Vsfold4: 0.670 MCFold: 0.534 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.658 RDfolder: 0.592 Sensitivity Vsfold4: 0.561 RDfolder: 0.491 Positive Predictive Value Vsfold4: 0.779 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.466 RNAwolf: 0.439 Sensitivity Vsfold4: 0.388 RNAwolf: 0.411 Positive Predictive Value Vsfold4: 0.568 RNAwolf: 0.478 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.614 CMfinder(20): 0.546 Sensitivity Vsfold4: 0.500 CMfinder(20): 0.366 Positive Predictive Value Vsfold4: 0.759 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.484 NanoFolder: 0.339 Sensitivity Vsfold4: 0.405 NanoFolder: 0.350 Positive Predictive Value Vsfold4: 0.585 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.645 Vsfold4: 0.493 Sensitivity Multilign(seed): 0.525 Vsfold4: 0.409 Positive Predictive Value Multilign(seed): 0.800 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.526 PPfold(seed): 0.079 Sensitivity Vsfold4: 0.432 PPfold(seed): 0.012 Positive Predictive Value Vsfold4: 0.648 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.510 RSpredict(seed): 0.268 Sensitivity Vsfold4: 0.437 RSpredict(seed): 0.129 Positive Predictive Value Vsfold4: 0.601 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.538 Carnac(seed): 0.251 Sensitivity Vsfold4: 0.458 Carnac(seed): 0.063 Positive Predictive Value Vsfold4: 0.637 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.525 Mastr(seed): 0.241 Sensitivity Vsfold4: 0.449 Mastr(seed): 0.065 Positive Predictive Value Vsfold4: 0.618 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold4: 0.167 Sensitivity PETfold_2.0(seed): 0.614 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold4: 0.167 Sensitivity PETfold_2.0(20): 0.509 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Murlet(seed)	20 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.604 Murlet(seed): 0.453 Sensitivity CentroidAlifold(20): 0.421 Murlet(seed): 0.238 Positive Predictive Value CentroidAlifold(20): 0.870 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	13 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.640 Murlet(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.508 Murlet(seed): 0.213 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	9 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.522 Murlet(seed): 0.400 Sensitivity ContextFold: 0.413 Murlet(seed): 0.225 Positive Predictive Value ContextFold: 0.665 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	30 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 Murlet(seed): 0.514 Sensitivity MXScarna(seed): 0.532 Murlet(seed): 0.315 Positive Predictive Value MXScarna(seed): 0.789 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.586 Murlet(seed): 0.463 Sensitivity RNAalifold(20): 0.428 Murlet(seed): 0.250 Positive Predictive Value RNAalifold(20): 0.807 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.69956606048e-08	8 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.449 Murlet(seed): 0.407 Sensitivity PETfold_pre2.0(20): 0.342 Murlet(seed): 0.195 Positive Predictive Value PETfold_pre2.0(20): 0.595 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.576 Murlet(seed): 0.457 Sensitivity PPfold(20): 0.423 Murlet(seed): 0.253 Positive Predictive Value PPfold(20): 0.790 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.570 Murlet(seed): 0.421 Sensitivity IPknot: 0.442 Murlet(seed): 0.241 Positive Predictive Value IPknot: 0.741 Murlet(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	33 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.677 Murlet(seed): 0.503 Sensitivity CentroidAlifold(seed): 0.517 Murlet(seed): 0.299 Positive Predictive Value CentroidAlifold(seed): 0.892 Murlet(seed): 0.851 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.581 Murlet(seed): 0.463 Sensitivity RNASampler(20): 0.429 Murlet(seed): 0.250 Positive Predictive Value RNASampler(20): 0.790 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	9 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 Murlet(seed): 0.457 Sensitivity TurboFold(20): 0.454 Murlet(seed): 0.253 Positive Predictive Value TurboFold(20): 0.751 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.599 Murlet(seed): 0.463 Sensitivity MXScarna(20): 0.479 Murlet(seed): 0.250 Positive Predictive Value MXScarna(20): 0.754 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.95070920198e-08	30 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.656 Murlet(seed): 0.514 Sensitivity Sfold: 0.549 Murlet(seed): 0.315 Positive Predictive Value Sfold: 0.788 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.556 Murlet(seed): 0.441 Sensitivity CentroidHomfold‑LAST: 0.472 Murlet(seed): 0.267 Positive Predictive Value CentroidHomfold‑LAST: 0.663 Murlet(seed): 0.738 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.49381627234e-08	30 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.647 Murlet(seed): 0.514 Sensitivity Contrafold: 0.569 Murlet(seed): 0.315 Positive Predictive Value Contrafold: 0.741 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.639 Murlet(seed): 0.514 Sensitivity RNAalifold(seed): 0.449 Murlet(seed): 0.315 Positive Predictive Value RNAalifold(seed): 0.914 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.615 Murlet(seed): 0.514 Sensitivity HotKnots: 0.552 Murlet(seed): 0.315 Positive Predictive Value HotKnots: 0.689 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.613 Murlet(seed): 0.512 Sensitivity MaxExpect: 0.533 Murlet(seed): 0.315 Positive Predictive Value MaxExpect: 0.711 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.619 Murlet(seed): 0.503 Sensitivity CentroidFold: 0.521 Murlet(seed): 0.299 Positive Predictive Value CentroidFold: 0.739 Murlet(seed): 0.851 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.615 Murlet(seed): 0.514 Sensitivity UNAFold: 0.543 Murlet(seed): 0.315 Positive Predictive Value UNAFold: 0.702 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.634 Murlet(seed): 0.514 Sensitivity PknotsRG: 0.566 Murlet(seed): 0.315 Positive Predictive Value PknotsRG: 0.715 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.550 Murlet(seed): 0.471 Sensitivity ProbKnot: 0.496 Murlet(seed): 0.271 Positive Predictive Value ProbKnot: 0.616 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	19 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.515 Murlet(seed): 0.463 Sensitivity Murlet(20): 0.359 Murlet(seed): 0.250 Positive Predictive Value Murlet(20): 0.744 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	30 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.631 Murlet(seed): 0.514 Sensitivity RNAfold: 0.561 Murlet(seed): 0.315 Positive Predictive Value RNAfold: 0.715 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.514 Murlet(seed): 0.463 Sensitivity Carnac(20): 0.283 Murlet(seed): 0.250 Positive Predictive Value Carnac(20): 0.939 Murlet(seed): 0.863 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.28439804626e-08	30 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.640 Murlet(seed): 0.514 Sensitivity RNAshapes: 0.568 Murlet(seed): 0.315 Positive Predictive Value RNAshapes: 0.726 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.599 Murlet(seed): 0.509 Sensitivity Fold: 0.543 Murlet(seed): 0.310 Positive Predictive Value Fold: 0.665 Murlet(seed): 0.842 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	10 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.518 Murlet(seed): 0.464 Sensitivity TurboFold(seed): 0.416 Murlet(seed): 0.268 Positive Predictive Value TurboFold(seed): 0.650 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.35568223474e-09	21 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.454 RSpredict(20): 0.416 Sensitivity Murlet(seed): 0.238 RSpredict(20): 0.309 Positive Predictive Value Murlet(seed): 0.869 RSpredict(20): 0.569 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	21 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.677 Murlet(seed): 0.545 Sensitivity Afold: 0.617 Murlet(seed): 0.357 Positive Predictive Value Afold: 0.747 Murlet(seed): 0.837 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	30 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.600 Murlet(seed): 0.514 Sensitivity RNAsubopt: 0.538 Murlet(seed): 0.315 Positive Predictive Value RNAsubopt: 0.674 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.426 Murlet(seed): 0.400 Sensitivity RNASLOpt: 0.352 Murlet(seed): 0.225 Positive Predictive Value RNASLOpt: 0.523 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	16 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.579 Murlet(seed): 0.479 Sensitivity Cylofold: 0.492 Murlet(seed): 0.287 Positive Predictive Value Cylofold: 0.687 Murlet(seed): 0.806 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	30 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.627 Murlet(seed): 0.514 Sensitivity McQFold: 0.544 Murlet(seed): 0.315 Positive Predictive Value McQFold: 0.728 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.460 Multilign(20): 0.431 Sensitivity Murlet(seed): 0.258 Multilign(20): 0.346 Positive Predictive Value Murlet(seed): 0.830 Multilign(20): 0.544 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.435 CRWrnafold: 0.419 Sensitivity Murlet(seed): 0.251 CRWrnafold: 0.377 Positive Predictive Value Murlet(seed): 0.759 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	30 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.588 Murlet(seed): 0.514 Sensitivity Pknots: 0.542 Murlet(seed): 0.315 Positive Predictive Value Pknots: 0.644 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Murlet(seed): 0.538 Sensitivity RNASampler(seed): 0.484 Murlet(seed): 0.349 Positive Predictive Value RNASampler(seed): 0.837 Murlet(seed): 0.833 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	17 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.758 Murlet(seed): 0.594 Sensitivity Alterna: 0.676 Murlet(seed): 0.425 Positive Predictive Value Alterna: 0.854 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	19 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.463 Mastr(20): 0.430 Sensitivity Murlet(seed): 0.250 Mastr(20): 0.237 Positive Predictive Value Murlet(seed): 0.863 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	28 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.546 Murlet(seed): 0.519 Sensitivity Vsfold4: 0.465 Murlet(seed): 0.323 Positive Predictive Value Vsfold4: 0.648 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08		= Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.522 Vsfold5: 0.518 Sensitivity Murlet(seed): 0.325 Vsfold5: 0.452 Positive Predictive Value Murlet(seed): 0.843 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.309965267453	+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.507 MCFold: 0.468 Sensitivity Murlet(seed): 0.305 MCFold: 0.484 Positive Predictive Value Murlet(seed): 0.848 MCFold: 0.459 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.578 RDfolder: 0.569 Sensitivity Murlet(seed): 0.397 RDfolder: 0.464 Positive Predictive Value Murlet(seed): 0.851 RDfolder: 0.707 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 1.1934089898e-05	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.418 RNAwolf: 0.348 Sensitivity Murlet(seed): 0.227 RNAwolf: 0.331 Positive Predictive Value Murlet(seed): 0.777 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	? CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.466 Murlet(seed): 0.148 Sensitivity CMfinder(20): 0.219 Murlet(seed): 0.094 Positive Predictive Value CMfinder(20): 1.000 Murlet(seed): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.404 NanoFolder: 0.252 Sensitivity Murlet(seed): 0.234 NanoFolder: 0.266 Positive Predictive Value Murlet(seed): 0.706 NanoFolder: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Murlet(seed): 0.446 Sensitivity Multilign(seed): 0.434 Murlet(seed): 0.262 Positive Predictive Value Multilign(seed): 0.725 Murlet(seed): 0.765 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.421 PPfold(seed): 0.124 Sensitivity Murlet(seed): 0.241 PPfold(seed): 0.030 Positive Predictive Value Murlet(seed): 0.742 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.503 RSpredict(seed): 0.402 Sensitivity Murlet(seed): 0.299 RSpredict(seed): 0.229 Positive Predictive Value Murlet(seed): 0.852 RSpredict(seed): 0.711 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.514 Carnac(seed): 0.262 Sensitivity Murlet(seed): 0.315 Carnac(seed): 0.069 Positive Predictive Value Murlet(seed): 0.846 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.514 Mastr(seed): 0.333 Sensitivity Murlet(seed): 0.315 Mastr(seed): 0.124 Positive Predictive Value Murlet(seed): 0.846 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Murlet(seed): 0.431 Sensitivity PETfold_2.0(seed): 0.684 Murlet(seed): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.897 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Vsfold5	38 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.681 Vsfold5: 0.404 Sensitivity CentroidAlifold(20): 0.527 Vsfold5: 0.345 Positive Predictive Value CentroidAlifold(20): 0.882 Vsfold5: 0.480 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.403 Sensitivity PETfold_pre2.0(seed): 0.606 Vsfold5: 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	39 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.674 Vsfold5: 0.433 Sensitivity ContextFold: 0.563 Vsfold5: 0.373 Positive Predictive Value ContextFold: 0.813 Vsfold5: 0.510 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.674 Vsfold5: 0.490 Sensitivity MXScarna(seed): 0.565 Vsfold5: 0.423 Positive Predictive Value MXScarna(seed): 0.808 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.666 Vsfold5: 0.417 Sensitivity RNAalifold(20): 0.512 Vsfold5: 0.355 Positive Predictive Value RNAalifold(20): 0.870 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold5: 0.378 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold5: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold5: 0.450 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	14 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.723 Vsfold5: 0.470 Sensitivity PPfold(20): 0.581 Vsfold5: 0.400 Positive Predictive Value PPfold(20): 0.905 Vsfold5: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.72523032126e-08	47 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.644 Vsfold5: 0.446 Sensitivity IPknot: 0.546 Vsfold5: 0.386 Positive Predictive Value IPknot: 0.765 Vsfold5: 0.524 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.592 Vsfold5: 0.468 Sensitivity CentroidAlifold(seed): 0.396 Vsfold5: 0.405 Positive Predictive Value CentroidAlifold(seed): 0.888 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.637 Vsfold5: 0.417 Sensitivity RNASampler(20): 0.482 Vsfold5: 0.355 Positive Predictive Value RNASampler(20): 0.846 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.681 Vsfold5: 0.470 Sensitivity TurboFold(20): 0.558 Vsfold5: 0.400 Positive Predictive Value TurboFold(20): 0.836 Vsfold5: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.89166989468e-09	33 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.635 Vsfold5: 0.417 Sensitivity MXScarna(20): 0.531 Vsfold5: 0.355 Positive Predictive Value MXScarna(20): 0.764 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.647 Vsfold5: 0.510 Sensitivity Sfold: 0.558 Vsfold5: 0.441 Positive Predictive Value Sfold: 0.755 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 Vsfold5: 0.452 Sensitivity CentroidHomfold‑LAST: 0.469 Vsfold5: 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.775 Vsfold5: 0.533 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.648 Vsfold5: 0.510 Sensitivity Contrafold: 0.580 Vsfold5: 0.441 Positive Predictive Value Contrafold: 0.730 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.603 Vsfold5: 0.483 Sensitivity RNAalifold(seed): 0.407 Vsfold5: 0.422 Positive Predictive Value RNAalifold(seed): 0.895 Vsfold5: 0.558 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.639 Vsfold5: 0.510 Sensitivity HotKnots: 0.575 Vsfold5: 0.441 Positive Predictive Value HotKnots: 0.715 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	107 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.630 Vsfold5: 0.500 Sensitivity MaxExpect: 0.561 Vsfold5: 0.432 Positive Predictive Value MaxExpect: 0.712 Vsfold5: 0.584 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	124 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.626 Vsfold5: 0.491 Sensitivity CentroidFold: 0.544 Vsfold5: 0.425 Positive Predictive Value CentroidFold: 0.726 Vsfold5: 0.574 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.637 Vsfold5: 0.510 Sensitivity UNAFold: 0.568 Vsfold5: 0.441 Positive Predictive Value UNAFold: 0.719 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.627 Vsfold5: 0.510 Sensitivity PknotsRG: 0.564 Vsfold5: 0.441 Positive Predictive Value PknotsRG: 0.701 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	83 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.619 Vsfold5: 0.492 Sensitivity ProbKnot: 0.566 Vsfold5: 0.427 Positive Predictive Value ProbKnot: 0.681 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.586 Vsfold5: 0.417 Sensitivity Murlet(20): 0.431 Vsfold5: 0.355 Positive Predictive Value Murlet(20): 0.801 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.630 Vsfold5: 0.510 Sensitivity RNAfold: 0.565 Vsfold5: 0.441 Positive Predictive Value RNAfold: 0.707 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.585 Vsfold5: 0.417 Sensitivity Carnac(20): 0.382 Vsfold5: 0.355 Positive Predictive Value Carnac(20): 0.900 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	127 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.623 Vsfold5: 0.510 Sensitivity RNAshapes: 0.555 Vsfold5: 0.441 Positive Predictive Value RNAshapes: 0.706 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.648 Vsfold5: 0.512 Sensitivity Fold: 0.586 Vsfold5: 0.445 Positive Predictive Value Fold: 0.720 Vsfold5: 0.595 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.566 Vsfold5: 0.380 Sensitivity TurboFold(seed): 0.467 Vsfold5: 0.326 Positive Predictive Value TurboFold(seed): 0.693 Vsfold5: 0.452 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.64481516727e-08	38 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.554 Vsfold5: 0.417 Sensitivity RSpredict(20): 0.433 Vsfold5: 0.358 Positive Predictive Value RSpredict(20): 0.713 Vsfold5: 0.493 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.623 Vsfold5: 0.518 Sensitivity Afold: 0.569 Vsfold5: 0.450 Positive Predictive Value Afold: 0.687 Vsfold5: 0.602 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.619 Vsfold5: 0.510 Sensitivity RNAsubopt: 0.557 Vsfold5: 0.441 Positive Predictive Value RNAsubopt: 0.693 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.553 Vsfold5: 0.433 Sensitivity RNASLOpt: 0.462 Vsfold5: 0.373 Positive Predictive Value RNASLOpt: 0.669 Vsfold5: 0.510 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.605 Vsfold5: 0.511 Sensitivity Cylofold: 0.516 Vsfold5: 0.442 Positive Predictive Value Cylofold: 0.716 Vsfold5: 0.599 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.604 Vsfold5: 0.507 Sensitivity McQFold: 0.523 Vsfold5: 0.439 Positive Predictive Value McQFold: 0.705 Vsfold5: 0.594 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.561 Vsfold5: 0.431 Sensitivity Multilign(20): 0.466 Vsfold5: 0.368 Positive Predictive Value Multilign(20): 0.682 Vsfold5: 0.513 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	31 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.580 Vsfold5: 0.454 Sensitivity CRWrnafold: 0.517 Vsfold5: 0.398 Positive Predictive Value CRWrnafold: 0.659 Vsfold5: 0.528 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.628 Vsfold5: 0.542 Sensitivity Pknots: 0.567 Vsfold5: 0.469 Positive Predictive Value Pknots: 0.703 Vsfold5: 0.634 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.663 Vsfold5: 0.632 Sensitivity RNASampler(seed): 0.515 Vsfold5: 0.571 Positive Predictive Value RNASampler(seed): 0.857 Vsfold5: 0.706 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.88234616094e-08	89 Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.665 Vsfold5: 0.623 Sensitivity Alterna: 0.599 Vsfold5: 0.542 Positive Predictive Value Alterna: 0.748 Vsfold5: 0.725 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold5: 0.417 Sensitivity Mastr(20): 0.354 Vsfold5: 0.355 Positive Predictive Value Mastr(20): 0.784 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.550 Vsfold5: 0.514 Sensitivity Vsfold4: 0.468 Vsfold5: 0.445 Positive Predictive Value Vsfold4: 0.653 Vsfold5: 0.600 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.522 Vsfold5: 0.518 Sensitivity Murlet(seed): 0.325 Vsfold5: 0.452 Positive Predictive Value Murlet(seed): 0.843 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.309965267453		= Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.542 MCFold: 0.539 Sensitivity Vsfold5: 0.471 MCFold: 0.559 Positive Predictive Value Vsfold5: 0.632 MCFold: 0.529 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 0.657358697881	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.634 RDfolder: 0.591 Sensitivity Vsfold5: 0.553 RDfolder: 0.489 Positive Predictive Value Vsfold5: 0.736 RDfolder: 0.723 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.434 Vsfold5: 0.427 Sensitivity RNAwolf: 0.406 Vsfold5: 0.369 Positive Predictive Value RNAwolf: 0.471 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 0.00297289556633	? CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.546 Vsfold5: 0.448 Sensitivity CMfinder(20): 0.366 Vsfold5: 0.360 Positive Predictive Value CMfinder(20): 0.822 Vsfold5: 0.567 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.428 NanoFolder: 0.358 Sensitivity Vsfold5: 0.372 NanoFolder: 0.368 Positive Predictive Value Vsfold5: 0.500 NanoFolder: 0.358 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.590 Vsfold5: 0.415 Sensitivity Multilign(seed): 0.470 Vsfold5: 0.350 Positive Predictive Value Multilign(seed): 0.748 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.438 PPfold(seed): 0.077 Sensitivity Vsfold5: 0.371 PPfold(seed): 0.011 Positive Predictive Value Vsfold5: 0.525 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.478 RSpredict(seed): 0.264 Sensitivity Vsfold5: 0.415 RSpredict(seed): 0.127 Positive Predictive Value Vsfold5: 0.557 RSpredict(seed): 0.557 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.503 Carnac(seed): 0.246 Sensitivity Vsfold5: 0.437 Carnac(seed): 0.061 Positive Predictive Value Vsfold5: 0.586 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.478 Mastr(seed): 0.239 Sensitivity Vsfold5: 0.412 Mastr(seed): 0.064 Positive Predictive Value Vsfold5: 0.559 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold5: 0.156 Sensitivity PETfold_2.0(seed): 0.614 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold5: 0.156 Sensitivity PETfold_2.0(20): 0.509 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MCFold	34 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.672 MCFold: 0.396 Sensitivity CentroidAlifold(20): 0.522 MCFold: 0.414 Positive Predictive Value CentroidAlifold(20): 0.869 MCFold: 0.387 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 MCFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.579 MCFold: 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.857 MCFold: 0.379 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	50 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.603 MCFold: 0.450 Sensitivity ContextFold: 0.506 MCFold: 0.460 Positive Predictive Value ContextFold: 0.724 MCFold: 0.448 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.658 MCFold: 0.461 Sensitivity MXScarna(seed): 0.547 MCFold: 0.479 Positive Predictive Value MXScarna(seed): 0.797 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.646 MCFold: 0.401 Sensitivity RNAalifold(20): 0.507 MCFold: 0.418 Positive Predictive Value RNAalifold(20): 0.826 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.628 MCFold: 0.382 Sensitivity PETfold_pre2.0(20): 0.512 MCFold: 0.393 Positive Predictive Value PETfold_pre2.0(20): 0.775 MCFold: 0.378 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	19 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.646 MCFold: 0.412 Sensitivity PPfold(20): 0.509 MCFold: 0.422 Positive Predictive Value PPfold(20): 0.824 MCFold: 0.411 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.7402423548e-08	58 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.610 MCFold: 0.455 Sensitivity IPknot: 0.517 MCFold: 0.466 Positive Predictive Value IPknot: 0.726 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.596 MCFold: 0.457 Sensitivity CentroidAlifold(seed): 0.396 MCFold: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.901 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.617 MCFold: 0.401 Sensitivity RNASampler(20): 0.482 MCFold: 0.418 Positive Predictive Value RNASampler(20): 0.795 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.616 MCFold: 0.412 Sensitivity TurboFold(20): 0.512 MCFold: 0.422 Positive Predictive Value TurboFold(20): 0.747 MCFold: 0.411 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	35 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.616 MCFold: 0.401 Sensitivity MXScarna(20): 0.514 MCFold: 0.418 Positive Predictive Value MXScarna(20): 0.742 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.663 MCFold: 0.522 Sensitivity Sfold: 0.574 MCFold: 0.535 Positive Predictive Value Sfold: 0.771 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.622 MCFold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.510 MCFold: 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.765 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.634 MCFold: 0.522 Sensitivity Contrafold: 0.568 MCFold: 0.535 Positive Predictive Value Contrafold: 0.713 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.608 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.408 MCFold: 0.492 Positive Predictive Value RNAalifold(seed): 0.909 MCFold: 0.467 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.643 MCFold: 0.522 Sensitivity HotKnots: 0.583 MCFold: 0.535 Positive Predictive Value HotKnots: 0.715 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	113 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.629 MCFold: 0.501 Sensitivity MaxExpect: 0.559 MCFold: 0.517 Positive Predictive Value MaxExpect: 0.713 MCFold: 0.495 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.630 MCFold: 0.510 Sensitivity CentroidFold: 0.546 MCFold: 0.525 Positive Predictive Value CentroidFold: 0.734 MCFold: 0.503 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.647 MCFold: 0.522 Sensitivity UNAFold: 0.579 MCFold: 0.535 Positive Predictive Value UNAFold: 0.730 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.643 MCFold: 0.522 Sensitivity PknotsRG: 0.580 MCFold: 0.535 Positive Predictive Value PknotsRG: 0.718 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.620 MCFold: 0.509 Sensitivity ProbKnot: 0.564 MCFold: 0.521 Positive Predictive Value ProbKnot: 0.687 MCFold: 0.505 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.592 MCFold: 0.401 Sensitivity Murlet(20): 0.448 MCFold: 0.418 Positive Predictive Value Murlet(20): 0.789 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.641 MCFold: 0.522 Sensitivity RNAfold: 0.577 MCFold: 0.535 Positive Predictive Value RNAfold: 0.718 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.592 MCFold: 0.401 Sensitivity Carnac(20): 0.393 MCFold: 0.418 Positive Predictive Value Carnac(20): 0.896 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.638 MCFold: 0.522 Sensitivity RNAshapes: 0.571 MCFold: 0.535 Positive Predictive Value RNAshapes: 0.719 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.639 MCFold: 0.526 Sensitivity Fold: 0.579 MCFold: 0.538 Positive Predictive Value Fold: 0.711 MCFold: 0.522 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.515 MCFold: 0.383 Sensitivity TurboFold(seed): 0.427 MCFold: 0.396 Positive Predictive Value TurboFold(seed): 0.627 MCFold: 0.377 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	35 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.563 MCFold: 0.401 Sensitivity RSpredict(20): 0.448 MCFold: 0.418 Positive Predictive Value RSpredict(20): 0.712 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.660 MCFold: 0.578 Sensitivity Afold: 0.605 MCFold: 0.599 Positive Predictive Value Afold: 0.727 MCFold: 0.565 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.625 MCFold: 0.522 Sensitivity RNAsubopt: 0.564 MCFold: 0.535 Positive Predictive Value RNAsubopt: 0.698 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.505 MCFold: 0.450 Sensitivity RNASLOpt: 0.414 MCFold: 0.460 Positive Predictive Value RNASLOpt: 0.622 MCFold: 0.448 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.641 MCFold: 0.543 Sensitivity Cylofold: 0.550 MCFold: 0.562 Positive Predictive Value Cylofold: 0.754 MCFold: 0.532 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.611 MCFold: 0.519 Sensitivity McQFold: 0.528 MCFold: 0.533 Positive Predictive Value McQFold: 0.713 MCFold: 0.514 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.512 MCFold: 0.413 Sensitivity Multilign(20): 0.425 MCFold: 0.426 Positive Predictive Value Multilign(20): 0.623 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	31 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.585 MCFold: 0.547 Sensitivity CRWrnafold: 0.525 MCFold: 0.579 Positive Predictive Value CRWrnafold: 0.659 MCFold: 0.525 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	131 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.588 MCFold: 0.522 Sensitivity Pknots: 0.535 MCFold: 0.535 Positive Predictive Value Pknots: 0.652 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.598 MCFold: 0.512 Sensitivity RNASampler(seed): 0.458 MCFold: 0.532 Positive Predictive Value RNASampler(seed): 0.786 MCFold: 0.498 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	86 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.681 MCFold: 0.606 Sensitivity Alterna: 0.614 MCFold: 0.624 Positive Predictive Value Alterna: 0.764 MCFold: 0.599 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.562 MCFold: 0.401 Sensitivity Mastr(20): 0.391 MCFold: 0.418 Positive Predictive Value Mastr(20): 0.811 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.562 MCFold: 0.539 Sensitivity Vsfold4: 0.477 MCFold: 0.552 Positive Predictive Value Vsfold4: 0.670 MCFold: 0.534 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.507 MCFold: 0.468 Sensitivity Murlet(seed): 0.305 MCFold: 0.484 Positive Predictive Value Murlet(seed): 0.848 MCFold: 0.459 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	124 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.542 MCFold: 0.539 Sensitivity Vsfold5: 0.471 MCFold: 0.559 Positive Predictive Value Vsfold5: 0.632 MCFold: 0.529 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 0.657358697881		- RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.619 MCFold: 0.599 Sensitivity RDfolder: 0.512 MCFold: 0.616 Positive Predictive Value RDfolder: 0.758 MCFold: 0.593 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 1.02208072244e-07	+ MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.455 RNAwolf: 0.410 Sensitivity MCFold: 0.466 RNAwolf: 0.388 Positive Predictive Value MCFold: 0.452 RNAwolf: 0.442 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.539 MCFold: 0.378 Sensitivity CMfinder(20): 0.389 MCFold: 0.392 Positive Predictive Value CMfinder(20): 0.751 MCFold: 0.373 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.84765843136e-09	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.475 NanoFolder: 0.377 Sensitivity MCFold: 0.473 NanoFolder: 0.395 Positive Predictive Value MCFold: 0.484 NanoFolder: 0.369 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.481 MCFold: 0.396 Sensitivity Multilign(seed): 0.366 MCFold: 0.392 Positive Predictive Value Multilign(seed): 0.641 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.396 PPfold(seed): 0.164 Sensitivity MCFold: 0.408 PPfold(seed): 0.039 Positive Predictive Value MCFold: 0.393 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.460 RSpredict(seed): 0.281 Sensitivity MCFold: 0.478 RSpredict(seed): 0.137 Positive Predictive Value MCFold: 0.450 RSpredict(seed): 0.586 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.476 Carnac(seed): 0.277 Sensitivity MCFold: 0.495 Carnac(seed): 0.077 Positive Predictive Value MCFold: 0.464 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.460 Mastr(seed): 0.251 Sensitivity MCFold: 0.478 Mastr(seed): 0.073 Positive Predictive Value MCFold: 0.450 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RDfolder	17 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.753 RDfolder: 0.541 Sensitivity CentroidAlifold(20): 0.602 RDfolder: 0.439 Positive Predictive Value CentroidAlifold(20): 0.946 RDfolder: 0.676 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	8 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RDfolder: 0.395 Sensitivity PETfold_pre2.0(seed): 0.588 RDfolder: 0.311 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.514 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	21 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.693 RDfolder: 0.491 Sensitivity ContextFold: 0.581 RDfolder: 0.389 Positive Predictive Value ContextFold: 0.835 RDfolder: 0.632 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	33 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.715 RDfolder: 0.548 Sensitivity MXScarna(seed): 0.599 RDfolder: 0.455 Positive Predictive Value MXScarna(seed): 0.859 RDfolder: 0.671 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.720 RDfolder: 0.541 Sensitivity RNAalifold(20): 0.564 RDfolder: 0.440 Positive Predictive Value RNAalifold(20): 0.924 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	5 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 RDfolder: 0.535 Sensitivity PETfold_pre2.0(20): 0.587 RDfolder: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.920 RDfolder: 0.704 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.720 RDfolder: 0.511 Sensitivity PPfold(20): 0.562 RDfolder: 0.386 Positive Predictive Value PPfold(20): 0.929 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	29 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.661 RDfolder: 0.500 Sensitivity IPknot: 0.559 RDfolder: 0.393 Positive Predictive Value IPknot: 0.791 RDfolder: 0.648 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 RDfolder: 0.548 Sensitivity CentroidAlifold(seed): 0.427 RDfolder: 0.454 Positive Predictive Value CentroidAlifold(seed): 0.873 RDfolder: 0.671 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.748 RDfolder: 0.541 Sensitivity RNASampler(20): 0.592 RDfolder: 0.440 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	8 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.676 RDfolder: 0.511 Sensitivity TurboFold(20): 0.541 RDfolder: 0.386 Positive Predictive Value TurboFold(20): 0.851 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.703 RDfolder: 0.541 Sensitivity MXScarna(20): 0.571 RDfolder: 0.440 Positive Predictive Value MXScarna(20): 0.871 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	96 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.709 RDfolder: 0.592 Sensitivity Sfold: 0.616 RDfolder: 0.491 Positive Predictive Value Sfold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.694 RDfolder: 0.534 Sensitivity CentroidHomfold‑LAST: 0.550 RDfolder: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.883 RDfolder: 0.684 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	96 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.724 RDfolder: 0.592 Sensitivity Contrafold: 0.643 RDfolder: 0.491 Positive Predictive Value Contrafold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.668 RDfolder: 0.580 Sensitivity RNAalifold(seed): 0.505 RDfolder: 0.474 Positive Predictive Value RNAalifold(seed): 0.891 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.715 RDfolder: 0.592 Sensitivity HotKnots: 0.644 RDfolder: 0.491 Positive Predictive Value HotKnots: 0.802 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.702 RDfolder: 0.586 Sensitivity MaxExpect: 0.625 RDfolder: 0.486 Positive Predictive Value MaxExpect: 0.795 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.729 RDfolder: 0.579 Sensitivity CentroidFold: 0.635 RDfolder: 0.480 Positive Predictive Value CentroidFold: 0.844 RDfolder: 0.709 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.709 RDfolder: 0.592 Sensitivity UNAFold: 0.631 RDfolder: 0.491 Positive Predictive Value UNAFold: 0.805 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.698 RDfolder: 0.592 Sensitivity PknotsRG: 0.626 RDfolder: 0.491 Positive Predictive Value PknotsRG: 0.787 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.708 RDfolder: 0.602 Sensitivity ProbKnot: 0.653 RDfolder: 0.506 Positive Predictive Value ProbKnot: 0.776 RDfolder: 0.726 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.646 RDfolder: 0.541 Sensitivity Murlet(20): 0.488 RDfolder: 0.440 Positive Predictive Value Murlet(20): 0.862 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	96 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.697 RDfolder: 0.592 Sensitivity RNAfold: 0.623 RDfolder: 0.491 Positive Predictive Value RNAfold: 0.788 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.616 RDfolder: 0.541 Sensitivity Carnac(20): 0.429 RDfolder: 0.440 Positive Predictive Value Carnac(20): 0.890 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	96 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.689 RDfolder: 0.592 Sensitivity RNAshapes: 0.609 RDfolder: 0.491 Positive Predictive Value RNAshapes: 0.786 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.726 RDfolder: 0.614 Sensitivity Fold: 0.658 RDfolder: 0.517 Positive Predictive Value Fold: 0.808 RDfolder: 0.740 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.598 RDfolder: 0.467 Sensitivity TurboFold(seed): 0.474 RDfolder: 0.352 Positive Predictive Value TurboFold(seed): 0.762 RDfolder: 0.633 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	18 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.642 RDfolder: 0.551 Sensitivity RSpredict(20): 0.493 RDfolder: 0.449 Positive Predictive Value RSpredict(20): 0.843 RDfolder: 0.686 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	74 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.704 RDfolder: 0.621 Sensitivity Afold: 0.641 RDfolder: 0.522 Positive Predictive Value Afold: 0.781 RDfolder: 0.748 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.689 RDfolder: 0.592 Sensitivity RNAsubopt: 0.614 RDfolder: 0.491 Positive Predictive Value RNAsubopt: 0.781 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.610 RDfolder: 0.491 Sensitivity RNASLOpt: 0.504 RDfolder: 0.389 Positive Predictive Value RNASLOpt: 0.747 RDfolder: 0.632 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	52 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.696 RDfolder: 0.582 Sensitivity Cylofold: 0.605 RDfolder: 0.487 Positive Predictive Value Cylofold: 0.809 RDfolder: 0.706 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.697 RDfolder: 0.592 Sensitivity McQFold: 0.596 RDfolder: 0.491 Positive Predictive Value McQFold: 0.822 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.623 RDfolder: 0.511 Sensitivity Multilign(20): 0.519 RDfolder: 0.386 Positive Predictive Value Multilign(20): 0.756 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	23 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.613 RDfolder: 0.465 Sensitivity CRWrnafold: 0.544 RDfolder: 0.365 Positive Predictive Value CRWrnafold: 0.701 RDfolder: 0.606 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	96 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.698 RDfolder: 0.592 Sensitivity Pknots: 0.628 RDfolder: 0.491 Positive Predictive Value Pknots: 0.783 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.734 RDfolder: 0.632 Sensitivity RNASampler(seed): 0.572 RDfolder: 0.518 Positive Predictive Value RNASampler(seed): 0.949 RDfolder: 0.779 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	88 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.668 RDfolder: 0.602 Sensitivity Alterna: 0.602 RDfolder: 0.502 Positive Predictive Value Alterna: 0.750 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.667 RDfolder: 0.541 Sensitivity Mastr(20): 0.516 RDfolder: 0.440 Positive Predictive Value Mastr(20): 0.868 RDfolder: 0.675 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	96 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.658 RDfolder: 0.592 Sensitivity Vsfold4: 0.561 RDfolder: 0.491 Positive Predictive Value Vsfold4: 0.779 RDfolder: 0.724 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.578 RDfolder: 0.569 Sensitivity Murlet(seed): 0.397 RDfolder: 0.464 Positive Predictive Value Murlet(seed): 0.851 RDfolder: 0.707 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 1.1934089898e-05	95 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.634 RDfolder: 0.591 Sensitivity Vsfold5: 0.553 RDfolder: 0.489 Positive Predictive Value Vsfold5: 0.736 RDfolder: 0.723 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	95 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.619 MCFold: 0.599 Sensitivity RDfolder: 0.512 MCFold: 0.616 Positive Predictive Value RDfolder: 0.758 MCFold: 0.593 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 1.02208072244e-07		- RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.557 RDfolder: 0.514 Sensitivity RNAwolf: 0.520 RDfolder: 0.403 Positive Predictive Value RNAwolf: 0.608 RDfolder: 0.668 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.48494289621e-08	? CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.751 RDfolder: 0.730 Sensitivity CMfinder(20): 0.567 RDfolder: 0.567 Positive Predictive Value CMfinder(20): 1.000 RDfolder: 0.944 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	- NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.495 RDfolder: 0.460 Sensitivity NanoFolder: 0.493 RDfolder: 0.378 Positive Predictive Value NanoFolder: 0.510 RDfolder: 0.572 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.00862119973e-08	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.645 RDfolder: 0.431 Sensitivity Multilign(seed): 0.525 RDfolder: 0.333 Positive Predictive Value Multilign(seed): 0.800 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.371 PPfold(seed): 0.121 Sensitivity RDfolder: 0.281 PPfold(seed): 0.020 Positive Predictive Value RDfolder: 0.503 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.04628667909e-08	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.554 RSpredict(seed): 0.418 Sensitivity RDfolder: 0.460 RSpredict(seed): 0.249 Positive Predictive Value RDfolder: 0.676 RSpredict(seed): 0.713 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.569 Carnac(seed): 0.338 Sensitivity RDfolder: 0.464 Carnac(seed): 0.116 Positive Predictive Value RDfolder: 0.707 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.548 Mastr(seed): 0.343 Sensitivity RDfolder: 0.455 Mastr(seed): 0.132 Positive Predictive Value RDfolder: 0.671 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAwolf	21 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.669 RNAwolf: 0.348 Sensitivity CentroidAlifold(20): 0.511 RNAwolf: 0.328 Positive Predictive Value CentroidAlifold(20): 0.880 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAwolf: 0.404 Sensitivity PETfold_pre2.0(seed): 0.602 RNAwolf: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	61 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.566 RNAwolf: 0.343 Sensitivity ContextFold: 0.469 RNAwolf: 0.318 Positive Predictive Value ContextFold: 0.684 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAwolf: 0.409 Sensitivity MXScarna(seed): 0.529 RNAwolf: 0.379 Positive Predictive Value MXScarna(seed): 0.770 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAwolf: 0.348 Sensitivity RNAalifold(20): 0.503 RNAwolf: 0.328 Positive Predictive Value RNAalifold(20): 0.829 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAwolf: 0.312 Sensitivity PETfold_pre2.0(20): 0.530 RNAwolf: 0.295 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAwolf: 0.338 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	20 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.663 RNAwolf: 0.343 Sensitivity PPfold(20): 0.528 RNAwolf: 0.325 Positive Predictive Value PPfold(20): 0.836 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	69 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.549 RNAwolf: 0.356 Sensitivity IPknot: 0.446 RNAwolf: 0.331 Positive Predictive Value IPknot: 0.678 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 RNAwolf: 0.416 Sensitivity CentroidAlifold(seed): 0.445 RNAwolf: 0.385 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.585 RNAwolf: 0.348 Sensitivity RNASampler(20): 0.448 RNAwolf: 0.328 Positive Predictive Value RNASampler(20): 0.768 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	20 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.616 RNAwolf: 0.343 Sensitivity TurboFold(20): 0.508 RNAwolf: 0.325 Positive Predictive Value TurboFold(20): 0.752 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	21 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.590 RNAwolf: 0.348 Sensitivity MXScarna(20): 0.486 RNAwolf: 0.328 Positive Predictive Value MXScarna(20): 0.720 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	69 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.506 RNAwolf: 0.356 Sensitivity Sfold: 0.428 RNAwolf: 0.331 Positive Predictive Value Sfold: 0.598 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.574 RNAwolf: 0.400 Sensitivity CentroidHomfold‑LAST: 0.439 RNAwolf: 0.372 Positive Predictive Value CentroidHomfold‑LAST: 0.755 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.500 RNAwolf: 0.356 Sensitivity Contrafold: 0.432 RNAwolf: 0.331 Positive Predictive Value Contrafold: 0.579 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNAwolf: 0.408 Sensitivity RNAalifold(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value RNAalifold(seed): 0.849 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.76499031155e-08	67 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.551 RNAwolf: 0.385 Sensitivity HotKnots: 0.489 RNAwolf: 0.360 Positive Predictive Value HotKnots: 0.627 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.485 RNAwolf: 0.356 Sensitivity MaxExpect: 0.421 RNAwolf: 0.331 Positive Predictive Value MaxExpect: 0.561 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.489 RNAwolf: 0.356 Sensitivity CentroidFold: 0.396 RNAwolf: 0.331 Positive Predictive Value CentroidFold: 0.606 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.483 RNAwolf: 0.356 Sensitivity UNAFold: 0.424 RNAwolf: 0.331 Positive Predictive Value UNAFold: 0.551 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.501 RNAwolf: 0.332 Sensitivity PknotsRG: 0.443 RNAwolf: 0.309 Positive Predictive Value PknotsRG: 0.568 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.482 RNAwolf: 0.356 Sensitivity ProbKnot: 0.423 RNAwolf: 0.331 Positive Predictive Value ProbKnot: 0.549 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.583 RNAwolf: 0.348 Sensitivity Murlet(20): 0.437 RNAwolf: 0.328 Positive Predictive Value Murlet(20): 0.784 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	69 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.485 RNAwolf: 0.356 Sensitivity RNAfold: 0.427 RNAwolf: 0.331 Positive Predictive Value RNAfold: 0.552 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.565 RNAwolf: 0.348 Sensitivity Carnac(20): 0.371 RNAwolf: 0.328 Positive Predictive Value Carnac(20): 0.867 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	67 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.517 RNAwolf: 0.385 Sensitivity RNAshapes: 0.452 RNAwolf: 0.360 Positive Predictive Value RNAshapes: 0.596 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.452 RNAwolf: 0.356 Sensitivity Fold: 0.402 RNAwolf: 0.331 Positive Predictive Value Fold: 0.511 RNAwolf: 0.386 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAwolf: 0.297 Sensitivity TurboFold(seed): 0.434 RNAwolf: 0.282 Positive Predictive Value TurboFold(seed): 0.650 RNAwolf: 0.321 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.13260312532e-08	20 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.520 RNAwolf: 0.343 Sensitivity RSpredict(20): 0.398 RNAwolf: 0.325 Positive Predictive Value RSpredict(20): 0.685 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.439 RNAwolf: 0.318 Sensitivity Afold: 0.397 RNAwolf: 0.298 Positive Predictive Value Afold: 0.488 RNAwolf: 0.342 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.532 RNAwolf: 0.385 Sensitivity RNAsubopt: 0.471 RNAwolf: 0.360 Positive Predictive Value RNAsubopt: 0.606 RNAwolf: 0.419 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.488 RNAwolf: 0.366 Sensitivity RNASLOpt: 0.395 RNAwolf: 0.342 Positive Predictive Value RNASLOpt: 0.607 RNAwolf: 0.397 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.529 RNAwolf: 0.433 Sensitivity Cylofold: 0.445 RNAwolf: 0.403 Positive Predictive Value Cylofold: 0.637 RNAwolf: 0.474 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.420 RNAwolf: 0.353 Sensitivity McQFold: 0.357 RNAwolf: 0.328 Positive Predictive Value McQFold: 0.495 RNAwolf: 0.382 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.534 RNAwolf: 0.366 Sensitivity Multilign(20): 0.449 RNAwolf: 0.345 Positive Predictive Value Multilign(20): 0.642 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	32 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.585 RNAwolf: 0.475 Sensitivity CRWrnafold: 0.522 RNAwolf: 0.449 Positive Predictive Value CRWrnafold: 0.663 RNAwolf: 0.513 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	64 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.506 RNAwolf: 0.427 Sensitivity Pknots: 0.456 RNAwolf: 0.401 Positive Predictive Value Pknots: 0.570 RNAwolf: 0.463 Number of pairs reference - predicted secondary structure: 64 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.417 RNAwolf: 0.340 Sensitivity RNASampler(seed): 0.283 RNAwolf: 0.333 Positive Predictive Value RNASampler(seed): 0.619 RNAwolf: 0.353 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	22 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.589 RNAwolf: 0.584 Sensitivity Alterna: 0.527 RNAwolf: 0.543 Positive Predictive Value Alterna: 0.669 RNAwolf: 0.639 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00321277492933	21 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.496 RNAwolf: 0.348 Sensitivity Mastr(20): 0.341 RNAwolf: 0.328 Positive Predictive Value Mastr(20): 0.729 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	60 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.466 RNAwolf: 0.439 Sensitivity Vsfold4: 0.388 RNAwolf: 0.411 Positive Predictive Value Vsfold4: 0.568 RNAwolf: 0.478 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.418 RNAwolf: 0.348 Sensitivity Murlet(seed): 0.227 RNAwolf: 0.331 Positive Predictive Value Murlet(seed): 0.777 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	58 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.434 Vsfold5: 0.427 Sensitivity RNAwolf: 0.406 Vsfold5: 0.369 Positive Predictive Value RNAwolf: 0.471 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 0.00297289556633	58 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.455 RNAwolf: 0.410 Sensitivity MCFold: 0.466 RNAwolf: 0.388 Positive Predictive Value MCFold: 0.452 RNAwolf: 0.442 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.557 RDfolder: 0.514 Sensitivity RNAwolf: 0.520 RDfolder: 0.403 Positive Predictive Value RNAwolf: 0.608 RDfolder: 0.668 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.48494289621e-08		- CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.521 RNAwolf: 0.370 Sensitivity CMfinder(20): 0.366 RNAwolf: 0.346 Positive Predictive Value CMfinder(20): 0.748 RNAwolf: 0.403 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.419 NanoFolder: 0.337 Sensitivity RNAwolf: 0.390 NanoFolder: 0.350 Positive Predictive Value RNAwolf: 0.459 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.556 RNAwolf: 0.374 Sensitivity Multilign(seed): 0.432 RNAwolf: 0.348 Positive Predictive Value Multilign(seed): 0.723 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.387 PPfold(seed): 0.148 Sensitivity RNAwolf: 0.363 PPfold(seed): 0.032 Positive Predictive Value RNAwolf: 0.422 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.415 RSpredict(seed): 0.395 Sensitivity RNAwolf: 0.385 RSpredict(seed): 0.246 Positive Predictive Value RNAwolf: 0.449 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.02521692575e-08	- Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.452 RNAwolf: 0.401 Sensitivity Carnac(seed): 0.229 RNAwolf: 0.373 Positive Predictive Value Carnac(seed): 0.890 RNAwolf: 0.432 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.2491108263e-05	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.389 Mastr(seed): 0.033 Sensitivity RNAwolf: 0.363 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.426 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAwolf: 0.549 Sensitivity PETfold_2.0(seed): 0.642 RNAwolf: 0.484 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAwolf: 0.630 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAwolf: 0.431 Sensitivity PETfold_2.0(20): 0.509 RNAwolf: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 RNAwolf: 0.512 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CMfinder(20)	11 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.667 CMfinder(20): 0.521 Sensitivity CentroidAlifold(20): 0.524 CMfinder(20): 0.366 Positive Predictive Value CentroidAlifold(20): 0.853 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	11 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(seed): 0.622 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(seed): 0.885 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.30295446166e-08	4 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.788 CMfinder(20): 0.546 Sensitivity ContextFold: 0.640 CMfinder(20): 0.366 Positive Predictive Value ContextFold: 0.972 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.652 CMfinder(20): 0.546 Sensitivity MXScarna(seed): 0.543 CMfinder(20): 0.366 Positive Predictive Value MXScarna(seed): 0.788 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.756 CMfinder(20): 0.546 Sensitivity RNAalifold(20): 0.591 CMfinder(20): 0.366 Positive Predictive Value RNAalifold(20): 0.970 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(20): 0.564 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(20): 0.826 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.35568223474e-09	4 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.788 CMfinder(20): 0.546 Sensitivity PPfold(20): 0.652 CMfinder(20): 0.366 Positive Predictive Value PPfold(20): 0.955 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.645 CMfinder(20): 0.546 Sensitivity IPknot: 0.549 CMfinder(20): 0.366 Positive Predictive Value IPknot: 0.763 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidAlifold(seed): 0.510 Sensitivity CMfinder(20): 0.366 CentroidAlifold(seed): 0.288 Positive Predictive Value CMfinder(20): 0.748 CentroidAlifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0014244499658	4 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.607 CMfinder(20): 0.546 Sensitivity RNASampler(20): 0.451 CMfinder(20): 0.366 Positive Predictive Value RNASampler(20): 0.822 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.743 CMfinder(20): 0.546 Sensitivity TurboFold(20): 0.610 CMfinder(20): 0.366 Positive Predictive Value TurboFold(20): 0.909 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.637 CMfinder(20): 0.546 Sensitivity MXScarna(20): 0.530 CMfinder(20): 0.366 Positive Predictive Value MXScarna(20): 0.770 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.618 CMfinder(20): 0.546 Sensitivity Sfold: 0.524 CMfinder(20): 0.366 Positive Predictive Value Sfold: 0.735 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.591 CMfinder(20): 0.546 Sensitivity CentroidHomfold‑LAST: 0.543 CMfinder(20): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.650 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.614 CMfinder(20): 0.546 Sensitivity Contrafold: 0.543 CMfinder(20): 0.366 Positive Predictive Value Contrafold: 0.701 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	1 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.727 CMfinder(20): 0.466 Sensitivity RNAalifold(seed): 0.531 CMfinder(20): 0.219 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: 0.579 CMfinder(20): 0.546 Sensitivity HotKnots: 0.500 CMfinder(20): 0.366 Positive Predictive Value HotKnots: 0.678 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.553 CMfinder(20): 0.546 Sensitivity MaxExpect: 0.470 CMfinder(20): 0.366 Positive Predictive Value MaxExpect: 0.658 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidFold: 0.393 Sensitivity CMfinder(20): 0.366 CentroidFold: 0.344 Positive Predictive Value CMfinder(20): 0.748 CentroidFold: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	4 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.570 CMfinder(20): 0.546 Sensitivity UNAFold: 0.494 CMfinder(20): 0.366 Positive Predictive Value UNAFold: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.570 CMfinder(20): 0.546 Sensitivity PknotsRG: 0.494 CMfinder(20): 0.366 Positive Predictive Value PknotsRG: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.582 CMfinder(20): 0.546 Sensitivity ProbKnot: 0.494 CMfinder(20): 0.366 Positive Predictive Value ProbKnot: 0.692 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.600 CMfinder(20): 0.546 Sensitivity Murlet(20): 0.463 CMfinder(20): 0.366 Positive Predictive Value Murlet(20): 0.784 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.570 CMfinder(20): 0.546 Sensitivity RNAfold: 0.494 CMfinder(20): 0.366 Positive Predictive Value RNAfold: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.567 CMfinder(20): 0.546 Sensitivity Carnac(20): 0.402 CMfinder(20): 0.366 Positive Predictive Value Carnac(20): 0.805 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: 0.556 CMfinder(20): 0.546 Sensitivity RNAshapes: 0.482 CMfinder(20): 0.366 Positive Predictive Value RNAshapes: 0.648 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.556 CMfinder(20): 0.546 Sensitivity Fold: 0.488 CMfinder(20): 0.366 Positive Predictive Value Fold: 0.640 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.566 CMfinder(20): 0.539 Sensitivity RSpredict(20): 0.443 CMfinder(20): 0.389 Positive Predictive Value RSpredict(20): 0.729 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	1 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.723 CMfinder(20): 0.577 Sensitivity Afold: 0.612 CMfinder(20): 0.388 Positive Predictive Value Afold: 0.857 CMfinder(20): 0.864 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.577 CMfinder(20): 0.546 Sensitivity RNAsubopt: 0.506 CMfinder(20): 0.366 Positive Predictive Value RNAsubopt: 0.664 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.635 CMfinder(20): 0.546 Sensitivity RNASLOpt: 0.512 CMfinder(20): 0.366 Positive Predictive Value RNASLOpt: 0.792 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.631 CMfinder(20): 0.546 Sensitivity Cylofold: 0.518 CMfinder(20): 0.366 Positive Predictive Value Cylofold: 0.773 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: 0.664 CMfinder(20): 0.546 Sensitivity McQFold: 0.530 CMfinder(20): 0.366 Positive Predictive Value McQFold: 0.837 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.578 CMfinder(20): 0.546 Sensitivity Multilign(20): 0.482 CMfinder(20): 0.366 Positive Predictive Value Multilign(20): 0.699 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.546 Pknots: 0.519 Sensitivity CMfinder(20): 0.366 Pknots: 0.439 Positive Predictive Value CMfinder(20): 0.822 Pknots: 0.621 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): 0.575 CMfinder(20): 0.546 Sensitivity Mastr(20): 0.421 CMfinder(20): 0.366 Positive Predictive Value Mastr(20): 0.793 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.614 CMfinder(20): 0.546 Sensitivity Vsfold4: 0.500 CMfinder(20): 0.366 Positive Predictive Value Vsfold4: 0.759 CMfinder(20): 0.822 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	1 CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.466 Murlet(seed): 0.148 Sensitivity CMfinder(20): 0.219 Murlet(seed): 0.094 Positive Predictive Value CMfinder(20): 1.000 Murlet(seed): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.546 Vsfold5: 0.448 Sensitivity CMfinder(20): 0.366 Vsfold5: 0.360 Positive Predictive Value CMfinder(20): 0.822 Vsfold5: 0.567 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	10 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.539 MCFold: 0.378 Sensitivity CMfinder(20): 0.389 MCFold: 0.392 Positive Predictive Value CMfinder(20): 0.751 MCFold: 0.373 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.84765843136e-09	1 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.751 RDfolder: 0.730 Sensitivity CMfinder(20): 0.567 RDfolder: 0.567 Positive Predictive Value CMfinder(20): 1.000 RDfolder: 0.944 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.521 RNAwolf: 0.370 Sensitivity CMfinder(20): 0.366 RNAwolf: 0.346 Positive Predictive Value CMfinder(20): 0.748 RNAwolf: 0.403 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09		? CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.507 NanoFolder: 0.183 Sensitivity CMfinder(20): 0.353 NanoFolder: 0.186 Positive Predictive Value CMfinder(20): 0.735 NanoFolder: 0.190 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.546 PPfold(seed): 0.000 Sensitivity CMfinder(20): 0.366 PPfold(seed): 0.000 Positive Predictive Value CMfinder(20): 0.822 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 RSpredict(seed): 0.015 Sensitivity CMfinder(20): 0.389 RSpredict(seed): 0.005 Positive Predictive Value CMfinder(20): 0.751 RSpredict(seed): 0.053 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	? CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.466 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.219 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.546 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.366 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.822 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CMfinder(20): 0.383 Sensitivity PETfold_2.0(seed): 0.614 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.946 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CMfinder(20): 0.383 Sensitivity PETfold_2.0(20): 0.509 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(20): 0.829 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
NanoFolder	14 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.664 NanoFolder: 0.269 Sensitivity CentroidAlifold(20): 0.516 NanoFolder: 0.280 Positive Predictive Value CentroidAlifold(20): 0.859 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.72523032126e-08	19 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 NanoFolder: 0.290 Sensitivity PETfold_pre2.0(seed): 0.605 NanoFolder: 0.301 Positive Predictive Value PETfold_pre2.0(seed): 0.885 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	25 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.622 NanoFolder: 0.339 Sensitivity ContextFold: 0.512 NanoFolder: 0.350 Positive Predictive Value ContextFold: 0.761 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	11 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.648 NanoFolder: 0.292 Sensitivity MXScarna(seed): 0.535 NanoFolder: 0.300 Positive Predictive Value MXScarna(seed): 0.790 NanoFolder: 0.294 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.77512146924e-08	7 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.669 NanoFolder: 0.276 Sensitivity RNAalifold(20): 0.527 NanoFolder: 0.286 Positive Predictive Value RNAalifold(20): 0.852 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	14 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.667 NanoFolder: 0.269 Sensitivity PETfold_pre2.0(20): 0.552 NanoFolder: 0.280 Positive Predictive Value PETfold_pre2.0(20): 0.810 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	7 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.719 NanoFolder: 0.276 Sensitivity PPfold(20): 0.590 NanoFolder: 0.286 Positive Predictive Value PPfold(20): 0.880 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.633 NanoFolder: 0.339 Sensitivity IPknot: 0.542 NanoFolder: 0.350 Positive Predictive Value IPknot: 0.743 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.536 NanoFolder: 0.290 Sensitivity CentroidAlifold(seed): 0.308 NanoFolder: 0.301 Positive Predictive Value CentroidAlifold(seed): 0.940 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.86109605532e-08	7 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.604 NanoFolder: 0.276 Sensitivity RNASampler(20): 0.458 NanoFolder: 0.286 Positive Predictive Value RNASampler(20): 0.801 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.651 NanoFolder: 0.276 Sensitivity TurboFold(20): 0.531 NanoFolder: 0.286 Positive Predictive Value TurboFold(20): 0.801 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.594 NanoFolder: 0.276 Sensitivity MXScarna(20): 0.505 NanoFolder: 0.286 Positive Predictive Value MXScarna(20): 0.704 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.579 NanoFolder: 0.339 Sensitivity Sfold: 0.493 NanoFolder: 0.350 Positive Predictive Value Sfold: 0.684 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.623 NanoFolder: 0.323 Sensitivity CentroidHomfold‑LAST: 0.497 NanoFolder: 0.333 Positive Predictive Value CentroidHomfold‑LAST: 0.787 NanoFolder: 0.322 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.574 NanoFolder: 0.339 Sensitivity Contrafold: 0.505 NanoFolder: 0.350 Positive Predictive Value Contrafold: 0.658 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	5 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.516 NanoFolder: 0.252 Sensitivity RNAalifold(seed): 0.331 NanoFolder: 0.266 Positive Predictive Value RNAalifold(seed): 0.810 NanoFolder: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	25 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.582 NanoFolder: 0.339 Sensitivity HotKnots: 0.518 NanoFolder: 0.350 Positive Predictive Value HotKnots: 0.660 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.587 NanoFolder: 0.339 Sensitivity MaxExpect: 0.512 NanoFolder: 0.350 Positive Predictive Value MaxExpect: 0.677 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	36 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.524 NanoFolder: 0.337 Sensitivity CentroidFold: 0.447 NanoFolder: 0.350 Positive Predictive Value CentroidFold: 0.621 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.556 NanoFolder: 0.339 Sensitivity UNAFold: 0.489 NanoFolder: 0.350 Positive Predictive Value UNAFold: 0.639 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.589 NanoFolder: 0.339 Sensitivity PknotsRG: 0.518 NanoFolder: 0.350 Positive Predictive Value PknotsRG: 0.675 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.589 NanoFolder: 0.339 Sensitivity ProbKnot: 0.527 NanoFolder: 0.350 Positive Predictive Value ProbKnot: 0.664 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	7 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.605 NanoFolder: 0.276 Sensitivity Murlet(20): 0.462 NanoFolder: 0.286 Positive Predictive Value Murlet(20): 0.797 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.590 NanoFolder: 0.339 Sensitivity RNAfold: 0.518 NanoFolder: 0.350 Positive Predictive Value RNAfold: 0.677 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.574 NanoFolder: 0.276 Sensitivity Carnac(20): 0.396 NanoFolder: 0.286 Positive Predictive Value Carnac(20): 0.837 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.557 NanoFolder: 0.339 Sensitivity RNAshapes: 0.491 NanoFolder: 0.350 Positive Predictive Value RNAshapes: 0.640 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.609 NanoFolder: 0.339 Sensitivity Fold: 0.537 NanoFolder: 0.350 Positive Predictive Value Fold: 0.696 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	5 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.439 NanoFolder: 0.341 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.351 Positive Predictive Value TurboFold(seed): 0.530 NanoFolder: 0.339 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	13 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.511 NanoFolder: 0.271 Sensitivity RSpredict(20): 0.394 NanoFolder: 0.286 Positive Predictive Value RSpredict(20): 0.667 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.58287649515e-08	17 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.546 NanoFolder: 0.386 Sensitivity Afold: 0.495 NanoFolder: 0.406 Positive Predictive Value Afold: 0.607 NanoFolder: 0.374 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	25 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.553 NanoFolder: 0.339 Sensitivity RNAsubopt: 0.493 NanoFolder: 0.350 Positive Predictive Value RNAsubopt: 0.627 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.530 NanoFolder: 0.339 Sensitivity RNASLOpt: 0.424 NanoFolder: 0.350 Positive Predictive Value RNASLOpt: 0.669 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.528 NanoFolder: 0.380 Sensitivity Cylofold: 0.447 NanoFolder: 0.387 Positive Predictive Value Cylofold: 0.631 NanoFolder: 0.383 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	24 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.493 NanoFolder: 0.327 Sensitivity McQFold: 0.424 NanoFolder: 0.338 Positive Predictive Value McQFold: 0.581 NanoFolder: 0.326 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	7 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.610 NanoFolder: 0.276 Sensitivity Multilign(20): 0.524 NanoFolder: 0.286 Positive Predictive Value Multilign(20): 0.715 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	14 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.584 NanoFolder: 0.475 Sensitivity CRWrnafold: 0.519 NanoFolder: 0.484 Positive Predictive Value CRWrnafold: 0.664 NanoFolder: 0.474 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	24 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.517 NanoFolder: 0.376 Sensitivity Pknots: 0.463 NanoFolder: 0.386 Positive Predictive Value Pknots: 0.584 NanoFolder: 0.377 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	3 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.318 NanoFolder: 0.169 Sensitivity RNASampler(seed): 0.215 NanoFolder: 0.194 Positive Predictive Value RNASampler(seed): 0.476 NanoFolder: 0.157 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.654 NanoFolder: 0.539 Sensitivity Alterna: 0.567 NanoFolder: 0.533 Positive Predictive Value Alterna: 0.764 NanoFolder: 0.557 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.505 NanoFolder: 0.276 Sensitivity Mastr(20): 0.370 NanoFolder: 0.286 Positive Predictive Value Mastr(20): 0.697 NanoFolder: 0.277 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.484 NanoFolder: 0.339 Sensitivity Vsfold4: 0.405 NanoFolder: 0.350 Positive Predictive Value Vsfold4: 0.585 NanoFolder: 0.338 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.404 NanoFolder: 0.252 Sensitivity Murlet(seed): 0.234 NanoFolder: 0.266 Positive Predictive Value Murlet(seed): 0.706 NanoFolder: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	22 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.428 NanoFolder: 0.358 Sensitivity Vsfold5: 0.372 NanoFolder: 0.368 Positive Predictive Value Vsfold5: 0.500 NanoFolder: 0.358 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.475 NanoFolder: 0.377 Sensitivity MCFold: 0.473 NanoFolder: 0.395 Positive Predictive Value MCFold: 0.484 NanoFolder: 0.369 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.495 RDfolder: 0.460 Sensitivity NanoFolder: 0.493 RDfolder: 0.378 Positive Predictive Value NanoFolder: 0.510 RDfolder: 0.572 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.00862119973e-08	36 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.419 NanoFolder: 0.337 Sensitivity RNAwolf: 0.390 NanoFolder: 0.350 Positive Predictive Value RNAwolf: 0.459 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.507 NanoFolder: 0.183 Sensitivity CMfinder(20): 0.353 NanoFolder: 0.186 Positive Predictive Value CMfinder(20): 0.735 NanoFolder: 0.190 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.586 NanoFolder: 0.302 Sensitivity Multilign(seed): 0.471 NanoFolder: 0.294 Positive Predictive Value Multilign(seed): 0.738 NanoFolder: 0.323 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.292 PPfold(seed): 0.096 Sensitivity NanoFolder: 0.300 PPfold(seed): 0.018 Positive Predictive Value NanoFolder: 0.294 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.293 RSpredict(seed): 0.091 Sensitivity NanoFolder: 0.307 RSpredict(seed): 0.037 Positive Predictive Value NanoFolder: 0.290 RSpredict(seed): 0.235 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.308 Carnac(seed): 0.138 Sensitivity NanoFolder: 0.317 Carnac(seed): 0.019 Positive Predictive Value NanoFolder: 0.308 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.292 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.300 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.294 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	? NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 NanoFolder: 0.243 Sensitivity PETfold_2.0(seed): 0.614 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(seed): 0.946 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.647 NanoFolder: 0.243 Sensitivity PETfold_2.0(20): 0.509 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(20): 0.829 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(seed)	6 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.571 Multilign(seed): 0.542 Sensitivity CentroidAlifold(20): 0.386 Multilign(seed): 0.413 Positive Predictive Value CentroidAlifold(20): 0.851 Multilign(seed): 0.719 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.658 Multilign(seed): 0.533 Sensitivity PETfold_pre2.0(seed): 0.510 Multilign(seed): 0.411 Positive Predictive Value PETfold_pre2.0(seed): 0.851 Multilign(seed): 0.698 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.517 Multilign(seed): 0.477 Sensitivity ContextFold: 0.421 Multilign(seed): 0.358 Positive Predictive Value ContextFold: 0.640 Multilign(seed): 0.642 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.560 Multilign(seed): 0.558 Sensitivity MXScarna(seed): 0.448 Multilign(seed): 0.434 Positive Predictive Value MXScarna(seed): 0.707 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.608 RNAalifold(20): 0.601 Sensitivity Multilign(seed): 0.468 RNAalifold(20): 0.463 Positive Predictive Value Multilign(seed): 0.795 RNAalifold(20): 0.786 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.443 Multilign(seed): 0.401 Sensitivity PETfold_pre2.0(20): 0.323 Multilign(seed): 0.283 Positive Predictive Value PETfold_pre2.0(20): 0.612 Multilign(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.613 Multilign(seed): 0.608 Sensitivity PPfold(20): 0.453 Multilign(seed): 0.468 Positive Predictive Value PPfold(20): 0.835 Multilign(seed): 0.795 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.604 Multilign(seed): 0.526 Sensitivity IPknot: 0.455 Multilign(seed): 0.402 Positive Predictive Value IPknot: 0.807 Multilign(seed): 0.695 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.643 Multilign(seed): 0.578 Sensitivity CentroidAlifold(seed): 0.454 Multilign(seed): 0.454 Positive Predictive Value CentroidAlifold(seed): 0.917 Multilign(seed): 0.743 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	5 Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.608 RNASampler(20): 0.597 Sensitivity Multilign(seed): 0.468 RNASampler(20): 0.447 Positive Predictive Value Multilign(seed): 0.795 RNASampler(20): 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.608 TurboFold(20): 0.605 Sensitivity Multilign(seed): 0.468 TurboFold(20): 0.468 Positive Predictive Value Multilign(seed): 0.795 TurboFold(20): 0.788 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.608 MXScarna(20): 0.580 Sensitivity Multilign(seed): 0.468 MXScarna(20): 0.468 Positive Predictive Value Multilign(seed): 0.795 MXScarna(20): 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.584 Multilign(seed): 0.558 Sensitivity Sfold: 0.462 Multilign(seed): 0.434 Positive Predictive Value Sfold: 0.746 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.612 Multilign(seed): 0.590 Sensitivity CentroidHomfold‑LAST: 0.509 Multilign(seed): 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.744 Multilign(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.602 Multilign(seed): 0.558 Sensitivity Contrafold: 0.500 Multilign(seed): 0.434 Positive Predictive Value Contrafold: 0.730 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.563 Multilign(seed): 0.558 Sensitivity RNAalifold(seed): 0.381 Multilign(seed): 0.434 Positive Predictive Value RNAalifold(seed): 0.838 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.558 HotKnots: 0.501 Sensitivity Multilign(seed): 0.434 HotKnots: 0.437 Positive Predictive Value Multilign(seed): 0.725 HotKnots: 0.581 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.580 Multilign(seed): 0.558 Sensitivity MaxExpect: 0.469 Multilign(seed): 0.434 Positive Predictive Value MaxExpect: 0.724 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.578 CentroidFold: 0.570 Sensitivity Multilign(seed): 0.454 CentroidFold: 0.443 Positive Predictive Value Multilign(seed): 0.743 CentroidFold: 0.738 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.41366350922e-05	8 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.558 UNAFold: 0.501 Sensitivity Multilign(seed): 0.434 UNAFold: 0.427 Positive Predictive Value Multilign(seed): 0.725 UNAFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.558 PknotsRG: 0.557 Sensitivity Multilign(seed): 0.434 PknotsRG: 0.476 Positive Predictive Value Multilign(seed): 0.725 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.564 Multilign(seed): 0.558 Sensitivity ProbKnot: 0.479 Multilign(seed): 0.434 Positive Predictive Value ProbKnot: 0.672 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Murlet(20): 0.586 Sensitivity Multilign(seed): 0.468 Murlet(20): 0.447 Positive Predictive Value Multilign(seed): 0.795 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.558 RNAfold: 0.555 Sensitivity Multilign(seed): 0.434 RNAfold: 0.476 Positive Predictive Value Multilign(seed): 0.725 RNAfold: 0.654 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Carnac(20): 0.507 Sensitivity Multilign(seed): 0.468 Carnac(20): 0.300 Positive Predictive Value Multilign(seed): 0.795 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.558 RNAshapes: 0.548 Sensitivity Multilign(seed): 0.434 RNAshapes: 0.472 Positive Predictive Value Multilign(seed): 0.725 RNAshapes: 0.643 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.558 Fold: 0.522 Sensitivity Multilign(seed): 0.434 Fold: 0.455 Positive Predictive Value Multilign(seed): 0.725 Fold: 0.607 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.563 Multilign(seed): 0.507 Sensitivity TurboFold(seed): 0.443 Multilign(seed): 0.386 Positive Predictive Value TurboFold(seed): 0.722 Multilign(seed): 0.674 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.542 RSpredict(20): 0.423 Sensitivity Multilign(seed): 0.413 RSpredict(20): 0.323 Positive Predictive Value Multilign(seed): 0.719 RSpredict(20): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.693 Afold: 0.680 Sensitivity Multilign(seed): 0.579 Afold: 0.596 Positive Predictive Value Multilign(seed): 0.835 Afold: 0.782 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.558 RNAsubopt: 0.555 Sensitivity Multilign(seed): 0.434 RNAsubopt: 0.476 Positive Predictive Value Multilign(seed): 0.725 RNAsubopt: 0.654 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.477 RNASLOpt: 0.400 Sensitivity Multilign(seed): 0.358 RNASLOpt: 0.316 Positive Predictive Value Multilign(seed): 0.642 RNASLOpt: 0.513 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.590 Cylofold: 0.541 Sensitivity Multilign(seed): 0.470 Cylofold: 0.436 Positive Predictive Value Multilign(seed): 0.748 Cylofold: 0.680 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.575 Multilign(seed): 0.558 Sensitivity McQFold: 0.472 Multilign(seed): 0.434 Positive Predictive Value McQFold: 0.707 Multilign(seed): 0.725 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Multilign(20): 0.661 Sensitivity Multilign(seed): 0.543 Multilign(20): 0.551 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.800 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.465 CRWrnafold: 0.443 Sensitivity Multilign(seed): 0.365 CRWrnafold: 0.375 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.558 Pknots: 0.494 Sensitivity Multilign(seed): 0.434 Pknots: 0.441 Positive Predictive Value Multilign(seed): 0.725 Pknots: 0.563 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.597 RNASampler(seed): 0.502 Sensitivity Multilign(seed): 0.476 RNASampler(seed): 0.332 Positive Predictive Value Multilign(seed): 0.756 RNASampler(seed): 0.767 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.624 Multilign(seed): 0.588 Sensitivity Alterna: 0.534 Multilign(seed): 0.483 Positive Predictive Value Alterna: 0.738 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.608 Mastr(20): 0.522 Sensitivity Multilign(seed): 0.468 Mastr(20): 0.342 Positive Predictive Value Multilign(seed): 0.795 Mastr(20): 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.645 Vsfold4: 0.493 Sensitivity Multilign(seed): 0.525 Vsfold4: 0.409 Positive Predictive Value Multilign(seed): 0.800 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Murlet(seed): 0.446 Sensitivity Multilign(seed): 0.434 Murlet(seed): 0.262 Positive Predictive Value Multilign(seed): 0.725 Murlet(seed): 0.765 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.590 Vsfold5: 0.415 Sensitivity Multilign(seed): 0.470 Vsfold5: 0.350 Positive Predictive Value Multilign(seed): 0.748 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.481 MCFold: 0.396 Sensitivity Multilign(seed): 0.366 MCFold: 0.392 Positive Predictive Value Multilign(seed): 0.641 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.645 RDfolder: 0.431 Sensitivity Multilign(seed): 0.525 RDfolder: 0.333 Positive Predictive Value Multilign(seed): 0.800 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.556 RNAwolf: 0.374 Sensitivity Multilign(seed): 0.432 RNAwolf: 0.348 Positive Predictive Value Multilign(seed): 0.723 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	0 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.586 NanoFolder: 0.302 Sensitivity Multilign(seed): 0.471 NanoFolder: 0.294 Positive Predictive Value Multilign(seed): 0.738 NanoFolder: 0.323 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0		? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.526 PPfold(seed): 0.152 Sensitivity Multilign(seed): 0.402 PPfold(seed): 0.038 Positive Predictive Value Multilign(seed): 0.695 PPfold(seed): 0.625 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.578 RSpredict(seed): 0.294 Sensitivity Multilign(seed): 0.454 RSpredict(seed): 0.152 Positive Predictive Value Multilign(seed): 0.743 RSpredict(seed): 0.578 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Carnac(seed): 0.283 Sensitivity Multilign(seed): 0.434 Carnac(seed): 0.080 Positive Predictive Value Multilign(seed): 0.725 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.434 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.725 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity Multilign(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PPfold(seed)	20 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(seed): 0.072 Sensitivity CentroidAlifold(20): 0.514 PPfold(seed): 0.012 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.81788725234e-08	24 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 PPfold(seed): 0.156 Sensitivity PETfold_pre2.0(seed): 0.594 PPfold(seed): 0.036 Positive Predictive Value PETfold_pre2.0(seed): 0.875 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	16 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.657 PPfold(seed): 0.100 Sensitivity ContextFold: 0.527 PPfold(seed): 0.019 Positive Predictive Value ContextFold: 0.824 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	19 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.627 PPfold(seed): 0.092 Sensitivity MXScarna(seed): 0.503 PPfold(seed): 0.016 Positive Predictive Value MXScarna(seed): 0.788 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	14 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.664 PPfold(seed): 0.061 Sensitivity RNAalifold(20): 0.515 PPfold(seed): 0.010 Positive Predictive Value RNAalifold(20): 0.862 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.30549897711e-08	17 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PPfold(seed): 0.077 Sensitivity PETfold_pre2.0(20): 0.532 PPfold(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	14 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.693 PPfold(seed): 0.061 Sensitivity PPfold(20): 0.548 PPfold(seed): 0.010 Positive Predictive Value PPfold(20): 0.880 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	19 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.629 PPfold(seed): 0.092 Sensitivity IPknot: 0.506 PPfold(seed): 0.016 Positive Predictive Value IPknot: 0.787 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.12160100812e-08	27 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.575 PPfold(seed): 0.148 Sensitivity CentroidAlifold(seed): 0.351 PPfold(seed): 0.032 Positive Predictive Value CentroidAlifold(seed): 0.947 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 PPfold(seed): 0.061 Sensitivity RNASampler(20): 0.460 PPfold(seed): 0.010 Positive Predictive Value RNASampler(20): 0.813 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.59816551561e-08	14 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.643 PPfold(seed): 0.061 Sensitivity TurboFold(20): 0.515 PPfold(seed): 0.010 Positive Predictive Value TurboFold(20): 0.809 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.47941000302e-08	14 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.596 PPfold(seed): 0.061 Sensitivity MXScarna(20): 0.483 PPfold(seed): 0.010 Positive Predictive Value MXScarna(20): 0.741 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	19 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.558 PPfold(seed): 0.092 Sensitivity Sfold: 0.449 PPfold(seed): 0.016 Positive Predictive Value Sfold: 0.699 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	18 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.616 PPfold(seed): 0.077 Sensitivity CentroidHomfold‑LAST: 0.523 PPfold(seed): 0.011 Positive Predictive Value CentroidHomfold‑LAST: 0.731 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	19 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.595 PPfold(seed): 0.092 Sensitivity Contrafold: 0.507 PPfold(seed): 0.016 Positive Predictive Value Contrafold: 0.703 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	11 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.563 PPfold(seed): 0.124 Sensitivity RNAalifold(seed): 0.366 PPfold(seed): 0.030 Positive Predictive Value RNAalifold(seed): 0.871 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.21732636221e-09	19 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.524 PPfold(seed): 0.092 Sensitivity HotKnots: 0.458 PPfold(seed): 0.016 Positive Predictive Value HotKnots: 0.605 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	19 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.544 PPfold(seed): 0.092 Sensitivity MaxExpect: 0.455 PPfold(seed): 0.016 Positive Predictive Value MaxExpect: 0.657 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	27 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.511 PPfold(seed): 0.148 Sensitivity CentroidFold: 0.426 PPfold(seed): 0.032 Positive Predictive Value CentroidFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.500 PPfold(seed): 0.092 Sensitivity UNAFold: 0.432 PPfold(seed): 0.016 Positive Predictive Value UNAFold: 0.587 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.04409141234e-08	19 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.573 PPfold(seed): 0.092 Sensitivity PknotsRG: 0.496 PPfold(seed): 0.016 Positive Predictive Value PknotsRG: 0.669 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.10198558684e-08	19 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.547 PPfold(seed): 0.092 Sensitivity ProbKnot: 0.478 PPfold(seed): 0.016 Positive Predictive Value ProbKnot: 0.632 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	14 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.569 PPfold(seed): 0.061 Sensitivity Murlet(20): 0.428 PPfold(seed): 0.010 Positive Predictive Value Murlet(20): 0.762 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	19 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.552 PPfold(seed): 0.092 Sensitivity RNAfold: 0.475 PPfold(seed): 0.016 Positive Predictive Value RNAfold: 0.648 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	14 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.558 PPfold(seed): 0.061 Sensitivity Carnac(20): 0.371 PPfold(seed): 0.010 Positive Predictive Value Carnac(20): 0.844 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	19 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.531 PPfold(seed): 0.092 Sensitivity RNAshapes: 0.458 PPfold(seed): 0.016 Positive Predictive Value RNAshapes: 0.622 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	19 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.532 PPfold(seed): 0.092 Sensitivity Fold: 0.466 PPfold(seed): 0.016 Positive Predictive Value Fold: 0.615 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	10 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.518 PPfold(seed): 0.127 Sensitivity TurboFold(seed): 0.413 PPfold(seed): 0.031 Positive Predictive Value TurboFold(seed): 0.656 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.33795641379e-09	20 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.520 PPfold(seed): 0.072 Sensitivity RSpredict(20): 0.398 PPfold(seed): 0.012 Positive Predictive Value RSpredict(20): 0.685 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	6 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.547 PPfold(seed): 0.138 Sensitivity Afold: 0.487 PPfold(seed): 0.036 Positive Predictive Value Afold: 0.621 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	19 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.539 PPfold(seed): 0.092 Sensitivity RNAsubopt: 0.469 PPfold(seed): 0.016 Positive Predictive Value RNAsubopt: 0.626 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	16 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.533 PPfold(seed): 0.100 Sensitivity RNASLOpt: 0.431 PPfold(seed): 0.019 Positive Predictive Value RNASLOpt: 0.666 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.45805449719e-08	16 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.594 PPfold(seed): 0.091 Sensitivity Cylofold: 0.490 PPfold(seed): 0.011 Positive Predictive Value Cylofold: 0.727 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08	19 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.568 PPfold(seed): 0.092 Sensitivity McQFold: 0.475 PPfold(seed): 0.016 Positive Predictive Value McQFold: 0.686 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	13 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.577 PPfold(seed): 0.020 Sensitivity Multilign(20): 0.488 PPfold(seed): 0.002 Positive Predictive Value Multilign(20): 0.688 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.57237423209e-08	9 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 PPfold(seed): 0.114 Sensitivity CRWrnafold: 0.472 PPfold(seed): 0.024 Positive Predictive Value CRWrnafold: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.511 PPfold(seed): 0.092 Sensitivity Pknots: 0.449 PPfold(seed): 0.016 Positive Predictive Value Pknots: 0.589 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	6 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.447 PPfold(seed): 0.160 Sensitivity RNASampler(seed): 0.299 PPfold(seed): 0.050 Positive Predictive Value RNASampler(seed): 0.673 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.566 PPfold(seed): 0.153 Sensitivity Alterna: 0.479 PPfold(seed): 0.032 Positive Predictive Value Alterna: 0.679 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	14 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.521 PPfold(seed): 0.061 Sensitivity Mastr(20): 0.352 PPfold(seed): 0.010 Positive Predictive Value Mastr(20): 0.778 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	17 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.526 PPfold(seed): 0.079 Sensitivity Vsfold4: 0.432 PPfold(seed): 0.012 Positive Predictive Value Vsfold4: 0.648 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	11 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.421 PPfold(seed): 0.124 Sensitivity Murlet(seed): 0.241 PPfold(seed): 0.030 Positive Predictive Value Murlet(seed): 0.742 PPfold(seed): 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	18 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.438 PPfold(seed): 0.077 Sensitivity Vsfold5: 0.371 PPfold(seed): 0.011 Positive Predictive Value Vsfold5: 0.525 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	22 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.396 PPfold(seed): 0.164 Sensitivity MCFold: 0.408 PPfold(seed): 0.039 Positive Predictive Value MCFold: 0.393 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	10 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.371 PPfold(seed): 0.121 Sensitivity RDfolder: 0.281 PPfold(seed): 0.020 Positive Predictive Value RDfolder: 0.503 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.04628667909e-08	27 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.387 PPfold(seed): 0.148 Sensitivity RNAwolf: 0.363 PPfold(seed): 0.032 Positive Predictive Value RNAwolf: 0.422 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	4 CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.546 PPfold(seed): 0.000 Sensitivity CMfinder(20): 0.366 PPfold(seed): 0.000 Positive Predictive Value CMfinder(20): 0.822 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.292 PPfold(seed): 0.096 Sensitivity NanoFolder: 0.300 PPfold(seed): 0.018 Positive Predictive Value NanoFolder: 0.294 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.95070920198e-08	7 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.526 PPfold(seed): 0.152 Sensitivity Multilign(seed): 0.402 PPfold(seed): 0.038 Positive Predictive Value Multilign(seed): 0.695 PPfold(seed): 0.625 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		= PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 RSpredict(seed): 0.147 Sensitivity PPfold(seed): 0.032 RSpredict(seed): 0.060 Positive Predictive Value PPfold(seed): 0.689 RSpredict(seed): 0.369 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.730582116292	+ PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.116 Carnac(seed): 0.097 Sensitivity PPfold(seed): 0.026 Carnac(seed): 0.009 Positive Predictive Value PPfold(seed): 0.524 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.19029237474e-08	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.092 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.016 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.524 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RSpredict(seed)	38 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 RSpredict(seed): 0.182 Sensitivity CentroidAlifold(20): 0.518 RSpredict(seed): 0.074 Positive Predictive Value CentroidAlifold(20): 0.877 RSpredict(seed): 0.454 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.688 RSpredict(seed): 0.416 Sensitivity PETfold_pre2.0(seed): 0.566 RSpredict(seed): 0.264 Positive Predictive Value PETfold_pre2.0(seed): 0.838 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.667 RSpredict(seed): 0.397 Sensitivity ContextFold: 0.551 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.809 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	60 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.661 RSpredict(seed): 0.378 Sensitivity MXScarna(seed): 0.554 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.790 RSpredict(seed): 0.645 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.645 RSpredict(seed): 0.191 Sensitivity RNAalifold(20): 0.499 RSpredict(seed): 0.079 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(seed): 0.294 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(seed): 0.144 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	21 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.662 RSpredict(seed): 0.153 Sensitivity PPfold(20): 0.526 RSpredict(seed): 0.060 Positive Predictive Value PPfold(20): 0.837 RSpredict(seed): 0.402 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.599 RSpredict(seed): 0.395 Sensitivity IPknot: 0.501 RSpredict(seed): 0.246 Positive Predictive Value IPknot: 0.717 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	60 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.626 RSpredict(seed): 0.373 Sensitivity CentroidAlifold(seed): 0.447 RSpredict(seed): 0.218 Positive Predictive Value CentroidAlifold(seed): 0.880 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.612 RSpredict(seed): 0.191 Sensitivity RNASampler(20): 0.471 RSpredict(seed): 0.079 Positive Predictive Value RNASampler(20): 0.798 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.625 RSpredict(seed): 0.153 Sensitivity TurboFold(20): 0.518 RSpredict(seed): 0.060 Positive Predictive Value TurboFold(20): 0.759 RSpredict(seed): 0.402 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	39 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.615 RSpredict(seed): 0.191 Sensitivity MXScarna(20): 0.514 RSpredict(seed): 0.079 Positive Predictive Value MXScarna(20): 0.740 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.565 RSpredict(seed): 0.375 Sensitivity Sfold: 0.486 RSpredict(seed): 0.220 Positive Predictive Value Sfold: 0.657 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.600 RSpredict(seed): 0.147 Sensitivity CentroidHomfold‑LAST: 0.512 RSpredict(seed): 0.061 Positive Predictive Value CentroidHomfold‑LAST: 0.710 RSpredict(seed): 0.362 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	61 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.589 RSpredict(seed): 0.375 Sensitivity Contrafold: 0.528 RSpredict(seed): 0.220 Positive Predictive Value Contrafold: 0.660 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.624 RSpredict(seed): 0.464 Sensitivity RNAalifold(seed): 0.448 RSpredict(seed): 0.306 Positive Predictive Value RNAalifold(seed): 0.871 RSpredict(seed): 0.703 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.571 RSpredict(seed): 0.266 Sensitivity HotKnots: 0.521 RSpredict(seed): 0.128 Positive Predictive Value HotKnots: 0.632 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.566 RSpredict(seed): 0.374 Sensitivity MaxExpect: 0.500 RSpredict(seed): 0.220 Positive Predictive Value MaxExpect: 0.642 RSpredict(seed): 0.637 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.579 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.498 RSpredict(seed): 0.218 Positive Predictive Value CentroidFold: 0.674 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.548 RSpredict(seed): 0.375 Sensitivity UNAFold: 0.488 RSpredict(seed): 0.220 Positive Predictive Value UNAFold: 0.616 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.588 RSpredict(seed): 0.266 Sensitivity PknotsRG: 0.533 RSpredict(seed): 0.128 Positive Predictive Value PknotsRG: 0.653 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.545 RSpredict(seed): 0.356 Sensitivity ProbKnot: 0.487 RSpredict(seed): 0.208 Positive Predictive Value ProbKnot: 0.610 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.581 RSpredict(seed): 0.191 Sensitivity Murlet(20): 0.431 RSpredict(seed): 0.079 Positive Predictive Value Murlet(20): 0.789 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.555 RSpredict(seed): 0.375 Sensitivity RNAfold: 0.498 RSpredict(seed): 0.220 Positive Predictive Value RNAfold: 0.621 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.580 RSpredict(seed): 0.191 Sensitivity Carnac(20): 0.376 RSpredict(seed): 0.079 Positive Predictive Value Carnac(20): 0.898 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.575 RSpredict(seed): 0.266 Sensitivity RNAshapes: 0.516 RSpredict(seed): 0.128 Positive Predictive Value RNAshapes: 0.646 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.555 RSpredict(seed): 0.373 Sensitivity Fold: 0.500 RSpredict(seed): 0.222 Positive Predictive Value Fold: 0.618 RSpredict(seed): 0.631 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.547 RSpredict(seed): 0.236 Sensitivity TurboFold(seed): 0.452 RSpredict(seed): 0.108 Positive Predictive Value TurboFold(seed): 0.667 RSpredict(seed): 0.524 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	40 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.535 RSpredict(seed): 0.280 Sensitivity RSpredict(20): 0.408 RSpredict(seed): 0.133 Positive Predictive Value RSpredict(20): 0.703 RSpredict(seed): 0.594 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.563 RSpredict(seed): 0.361 Sensitivity Afold: 0.524 RSpredict(seed): 0.197 Positive Predictive Value Afold: 0.609 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.568 RSpredict(seed): 0.266 Sensitivity RNAsubopt: 0.517 RSpredict(seed): 0.128 Positive Predictive Value RNAsubopt: 0.628 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 RSpredict(seed): 0.115 Sensitivity RNASLOpt: 0.413 RSpredict(seed): 0.046 Positive Predictive Value RNASLOpt: 0.615 RSpredict(seed): 0.294 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	29 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.611 RSpredict(seed): 0.231 Sensitivity Cylofold: 0.523 RSpredict(seed): 0.109 Positive Predictive Value Cylofold: 0.719 RSpredict(seed): 0.500 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.531 RSpredict(seed): 0.375 Sensitivity McQFold: 0.462 RSpredict(seed): 0.220 Positive Predictive Value McQFold: 0.613 RSpredict(seed): 0.642 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.526 RSpredict(seed): 0.170 Sensitivity Multilign(20): 0.437 RSpredict(seed): 0.067 Positive Predictive Value Multilign(20): 0.640 RSpredict(seed): 0.439 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	9 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 RSpredict(seed): 0.108 Sensitivity CRWrnafold: 0.472 RSpredict(seed): 0.042 Positive Predictive Value CRWrnafold: 0.616 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	58 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.567 RSpredict(seed): 0.276 Sensitivity Pknots: 0.516 RSpredict(seed): 0.134 Positive Predictive Value Pknots: 0.629 RSpredict(seed): 0.576 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.594 RSpredict(seed): 0.467 Sensitivity RNASampler(seed): 0.448 RSpredict(seed): 0.298 Positive Predictive Value RNASampler(seed): 0.793 RSpredict(seed): 0.737 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.655 RSpredict(seed): 0.435 Sensitivity Alterna: 0.587 RSpredict(seed): 0.264 Positive Predictive Value Alterna: 0.737 RSpredict(seed): 0.729 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	39 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.515 RSpredict(seed): 0.191 Sensitivity Mastr(20): 0.345 RSpredict(seed): 0.079 Positive Predictive Value Mastr(20): 0.773 RSpredict(seed): 0.472 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.510 RSpredict(seed): 0.268 Sensitivity Vsfold4: 0.437 RSpredict(seed): 0.129 Positive Predictive Value Vsfold4: 0.601 RSpredict(seed): 0.561 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.503 RSpredict(seed): 0.402 Sensitivity Murlet(seed): 0.299 RSpredict(seed): 0.229 Positive Predictive Value Murlet(seed): 0.852 RSpredict(seed): 0.711 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.478 RSpredict(seed): 0.264 Sensitivity Vsfold5: 0.415 RSpredict(seed): 0.127 Positive Predictive Value Vsfold5: 0.557 RSpredict(seed): 0.557 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.460 RSpredict(seed): 0.281 Sensitivity MCFold: 0.478 RSpredict(seed): 0.137 Positive Predictive Value MCFold: 0.450 RSpredict(seed): 0.586 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.554 RSpredict(seed): 0.418 Sensitivity RDfolder: 0.460 RSpredict(seed): 0.249 Positive Predictive Value RDfolder: 0.676 RSpredict(seed): 0.713 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.415 RSpredict(seed): 0.395 Sensitivity RNAwolf: 0.385 RSpredict(seed): 0.246 Positive Predictive Value RNAwolf: 0.449 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.02521692575e-08	10 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 RSpredict(seed): 0.015 Sensitivity CMfinder(20): 0.389 RSpredict(seed): 0.005 Positive Predictive Value CMfinder(20): 0.751 RSpredict(seed): 0.053 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	18 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.293 RSpredict(seed): 0.091 Sensitivity NanoFolder: 0.307 RSpredict(seed): 0.037 Positive Predictive Value NanoFolder: 0.290 RSpredict(seed): 0.235 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	11 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.578 RSpredict(seed): 0.294 Sensitivity Multilign(seed): 0.454 RSpredict(seed): 0.152 Positive Predictive Value Multilign(seed): 0.743 RSpredict(seed): 0.578 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	27 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 RSpredict(seed): 0.147 Sensitivity PPfold(seed): 0.032 RSpredict(seed): 0.060 Positive Predictive Value PPfold(seed): 0.689 RSpredict(seed): 0.369 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.730582116292		+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.466 Carnac(seed): 0.401 Sensitivity RSpredict(seed): 0.309 Carnac(seed): 0.178 Positive Predictive Value RSpredict(seed): 0.705 Carnac(seed): 0.908 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.266 Mastr(seed): 0.221 Sensitivity RSpredict(seed): 0.128 Mastr(seed): 0.057 Positive Predictive Value RSpredict(seed): 0.561 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RSpredict(seed): 0.513 Sensitivity PETfold_2.0(seed): 0.684 RSpredict(seed): 0.289 Positive Predictive Value PETfold_2.0(seed): 0.897 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Carnac(seed)	24 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.632 Carnac(seed): 0.146 Sensitivity CentroidAlifold(20): 0.464 Carnac(seed): 0.021 Positive Predictive Value CentroidAlifold(20): 0.864 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.687 Carnac(seed): 0.467 Sensitivity PETfold_pre2.0(seed): 0.577 Carnac(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	11 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.672 Carnac(seed): 0.479 Sensitivity ContextFold: 0.553 Carnac(seed): 0.260 Positive Predictive Value ContextFold: 0.816 Carnac(seed): 0.882 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	35 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.661 Carnac(seed): 0.404 Sensitivity MXScarna(seed): 0.560 Carnac(seed): 0.181 Positive Predictive Value MXScarna(seed): 0.781 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.617 Carnac(seed): 0.186 Sensitivity RNAalifold(20): 0.466 Carnac(seed): 0.035 Positive Predictive Value RNAalifold(20): 0.820 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	9 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.516 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.400 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.670 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.609 Carnac(seed): 0.233 Sensitivity PPfold(20): 0.455 Carnac(seed): 0.055 Positive Predictive Value PPfold(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61680779366e-09	13 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.601 Carnac(seed): 0.461 Sensitivity IPknot: 0.495 Carnac(seed): 0.241 Positive Predictive Value IPknot: 0.730 Carnac(seed): 0.882 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.29976619895e-09	38 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Carnac(seed): 0.396 Sensitivity CentroidAlifold(seed): 0.529 Carnac(seed): 0.173 Positive Predictive Value CentroidAlifold(seed): 0.883 Carnac(seed): 0.905 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.613 Carnac(seed): 0.186 Sensitivity RNASampler(20): 0.460 Carnac(seed): 0.035 Positive Predictive Value RNASampler(20): 0.820 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.89920829651e-08	10 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.600 Carnac(seed): 0.233 Sensitivity TurboFold(20): 0.473 Carnac(seed): 0.055 Positive Predictive Value TurboFold(20): 0.766 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.88760648134e-09	23 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.612 Carnac(seed): 0.186 Sensitivity MXScarna(20): 0.505 Carnac(seed): 0.035 Positive Predictive Value MXScarna(20): 0.746 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	35 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.593 Carnac(seed): 0.404 Sensitivity Sfold: 0.508 Carnac(seed): 0.181 Positive Predictive Value Sfold: 0.695 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.572 Carnac(seed): 0.242 Sensitivity CentroidHomfold‑LAST: 0.483 Carnac(seed): 0.059 Positive Predictive Value CentroidHomfold‑LAST: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.16590079822e-09	35 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.621 Carnac(seed): 0.404 Sensitivity Contrafold: 0.548 Carnac(seed): 0.181 Positive Predictive Value Contrafold: 0.704 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.661 Carnac(seed): 0.425 Sensitivity RNAalifold(seed): 0.501 Carnac(seed): 0.201 Positive Predictive Value RNAalifold(seed): 0.872 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.626 Carnac(seed): 0.241 Sensitivity HotKnots: 0.565 Carnac(seed): 0.058 Positive Predictive Value HotKnots: 0.698 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.579 Carnac(seed): 0.402 Sensitivity MaxExpect: 0.507 Carnac(seed): 0.180 Positive Predictive Value MaxExpect: 0.661 Carnac(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.603 Carnac(seed): 0.396 Sensitivity CentroidFold: 0.512 Carnac(seed): 0.173 Positive Predictive Value CentroidFold: 0.712 Carnac(seed): 0.905 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.570 Carnac(seed): 0.404 Sensitivity UNAFold: 0.504 Carnac(seed): 0.181 Positive Predictive Value UNAFold: 0.647 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.632 Carnac(seed): 0.241 Sensitivity PknotsRG: 0.568 Carnac(seed): 0.058 Positive Predictive Value PknotsRG: 0.708 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.546 Carnac(seed): 0.412 Sensitivity ProbKnot: 0.483 Carnac(seed): 0.191 Positive Predictive Value ProbKnot: 0.619 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.557 Carnac(seed): 0.186 Sensitivity Murlet(20): 0.401 Carnac(seed): 0.035 Positive Predictive Value Murlet(20): 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.571 Carnac(seed): 0.404 Sensitivity RNAfold: 0.507 Carnac(seed): 0.181 Positive Predictive Value RNAfold: 0.645 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.563 Carnac(seed): 0.186 Sensitivity Carnac(20): 0.345 Carnac(seed): 0.035 Positive Predictive Value Carnac(20): 0.926 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	34 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.637 Carnac(seed): 0.241 Sensitivity RNAshapes: 0.569 Carnac(seed): 0.058 Positive Predictive Value RNAshapes: 0.719 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.548 Carnac(seed): 0.426 Sensitivity Fold: 0.492 Carnac(seed): 0.202 Positive Predictive Value Fold: 0.611 Carnac(seed): 0.900 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	11 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.544 Carnac(seed): 0.248 Sensitivity TurboFold(seed): 0.439 Carnac(seed): 0.062 Positive Predictive Value TurboFold(seed): 0.679 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	25 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.466 Carnac(seed): 0.179 Sensitivity RSpredict(20): 0.355 Carnac(seed): 0.032 Positive Predictive Value RSpredict(20): 0.618 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.668 Carnac(seed): 0.302 Sensitivity Afold: 0.614 Carnac(seed): 0.092 Positive Predictive Value Afold: 0.732 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	34 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.614 Carnac(seed): 0.241 Sensitivity RNAsubopt: 0.553 Carnac(seed): 0.058 Positive Predictive Value RNAsubopt: 0.686 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	10 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.462 Carnac(seed): 0.107 Sensitivity RNASLOpt: 0.378 Carnac(seed): 0.012 Positive Predictive Value RNASLOpt: 0.572 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	18 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.601 Carnac(seed): 0.193 Sensitivity Cylofold: 0.510 Carnac(seed): 0.037 Positive Predictive Value Cylofold: 0.715 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	35 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.554 Carnac(seed): 0.404 Sensitivity McQFold: 0.479 Carnac(seed): 0.181 Positive Predictive Value McQFold: 0.643 Carnac(seed): 0.903 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.476 Carnac(seed): 0.237 Sensitivity Multilign(20): 0.386 Carnac(seed): 0.056 Positive Predictive Value Multilign(20): 0.596 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.01499922709e-08	7 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 Carnac(seed): 0.132 Sensitivity CRWrnafold: 0.428 Carnac(seed): 0.017 Positive Predictive Value CRWrnafold: 0.554 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	34 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.578 Carnac(seed): 0.241 Sensitivity Pknots: 0.532 Carnac(seed): 0.058 Positive Predictive Value Pknots: 0.634 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Carnac(seed): 0.346 Sensitivity RNASampler(seed): 0.484 Carnac(seed): 0.120 Positive Predictive Value RNASampler(seed): 0.837 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	17 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.758 Carnac(seed): 0.382 Sensitivity Alterna: 0.676 Carnac(seed): 0.147 Positive Predictive Value Alterna: 0.854 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	23 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.498 Carnac(seed): 0.186 Sensitivity Mastr(20): 0.320 Carnac(seed): 0.035 Positive Predictive Value Mastr(20): 0.780 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	32 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.538 Carnac(seed): 0.251 Sensitivity Vsfold4: 0.458 Carnac(seed): 0.063 Positive Predictive Value Vsfold4: 0.637 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.514 Carnac(seed): 0.262 Sensitivity Murlet(seed): 0.315 Carnac(seed): 0.069 Positive Predictive Value Murlet(seed): 0.846 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.503 Carnac(seed): 0.246 Sensitivity Vsfold5: 0.437 Carnac(seed): 0.061 Positive Predictive Value Vsfold5: 0.586 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.476 Carnac(seed): 0.277 Sensitivity MCFold: 0.495 Carnac(seed): 0.077 Positive Predictive Value MCFold: 0.464 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.569 Carnac(seed): 0.338 Sensitivity RDfolder: 0.464 Carnac(seed): 0.116 Positive Predictive Value RDfolder: 0.707 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.452 RNAwolf: 0.401 Sensitivity Carnac(seed): 0.229 RNAwolf: 0.373 Positive Predictive Value Carnac(seed): 0.890 RNAwolf: 0.432 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.2491108263e-05	1 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.466 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.219 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	6 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.308 Carnac(seed): 0.138 Sensitivity NanoFolder: 0.317 Carnac(seed): 0.019 Positive Predictive Value NanoFolder: 0.308 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Carnac(seed): 0.283 Sensitivity Multilign(seed): 0.434 Carnac(seed): 0.080 Positive Predictive Value Multilign(seed): 0.725 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	12 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.116 Carnac(seed): 0.097 Sensitivity PPfold(seed): 0.026 Carnac(seed): 0.009 Positive Predictive Value PPfold(seed): 0.524 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.19029237474e-08	39 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.466 Carnac(seed): 0.401 Sensitivity RSpredict(seed): 0.309 Carnac(seed): 0.178 Positive Predictive Value RSpredict(seed): 0.705 Carnac(seed): 0.908 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.306 Carnac(seed): 0.241 Sensitivity Mastr(seed): 0.105 Carnac(seed): 0.058 Positive Predictive Value Mastr(seed): 0.900 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	? CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(seed)	39 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.673 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.516 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.879 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Mastr(seed): 0.034 Sensitivity PETfold_pre2.0(seed): 0.595 Mastr(seed): 0.003 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	16 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.657 Mastr(seed): 0.000 Sensitivity ContextFold: 0.527 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.824 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.02510705504e-08	52 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.666 Mastr(seed): 0.239 Sensitivity MXScarna(seed): 0.554 Mastr(seed): 0.064 Positive Predictive Value MXScarna(seed): 0.804 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.502 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.860 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	15 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.691 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.544 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.881 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	19 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.629 Mastr(seed): 0.000 Sensitivity IPknot: 0.506 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.787 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	60 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.593 Mastr(seed): 0.219 Sensitivity CentroidAlifold(seed): 0.397 Mastr(seed): 0.055 Positive Predictive Value CentroidAlifold(seed): 0.889 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.623 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.470 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.830 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.655 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.529 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.816 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	34 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.624 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.756 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	53 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.601 Mastr(seed): 0.236 Sensitivity Sfold: 0.513 Mastr(seed): 0.062 Positive Predictive Value Sfold: 0.707 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.626 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.534 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.740 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.22210847902e-08	53 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.596 Mastr(seed): 0.236 Sensitivity Contrafold: 0.536 Mastr(seed): 0.062 Positive Predictive Value Contrafold: 0.668 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.596 Mastr(seed): 0.297 Sensitivity RNAalifold(seed): 0.397 Mastr(seed): 0.099 Positive Predictive Value RNAalifold(seed): 0.897 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	53 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.578 Mastr(seed): 0.236 Sensitivity HotKnots: 0.524 Mastr(seed): 0.062 Positive Predictive Value HotKnots: 0.643 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.600 Mastr(seed): 0.247 Sensitivity MaxExpect: 0.532 Mastr(seed): 0.068 Positive Predictive Value MaxExpect: 0.682 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.579 Mastr(seed): 0.219 Sensitivity CentroidFold: 0.501 Mastr(seed): 0.055 Positive Predictive Value CentroidFold: 0.674 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.582 Mastr(seed): 0.236 Sensitivity UNAFold: 0.520 Mastr(seed): 0.062 Positive Predictive Value UNAFold: 0.655 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.591 Mastr(seed): 0.236 Sensitivity PknotsRG: 0.533 Mastr(seed): 0.062 Positive Predictive Value PknotsRG: 0.659 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.573 Mastr(seed): 0.186 Sensitivity ProbKnot: 0.523 Mastr(seed): 0.035 Positive Predictive Value ProbKnot: 0.633 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.577 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.423 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.791 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.590 Mastr(seed): 0.236 Sensitivity RNAfold: 0.531 Mastr(seed): 0.062 Positive Predictive Value RNAfold: 0.660 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.577 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.372 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.897 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.580 Mastr(seed): 0.236 Sensitivity RNAshapes: 0.518 Mastr(seed): 0.062 Positive Predictive Value RNAshapes: 0.654 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.609 Mastr(seed): 0.247 Sensitivity Fold: 0.552 Mastr(seed): 0.069 Positive Predictive Value Fold: 0.676 Mastr(seed): 0.886 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.544 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.439 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.679 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.02533530638e-08	39 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.544 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.425 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.701 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.570 Mastr(seed): 0.293 Sensitivity Afold: 0.526 Mastr(seed): 0.096 Positive Predictive Value Afold: 0.621 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.564 Mastr(seed): 0.236 Sensitivity RNAsubopt: 0.511 Mastr(seed): 0.062 Positive Predictive Value RNAsubopt: 0.626 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.533 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.431 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.666 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.48055519165e-08	28 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.617 Mastr(seed): 0.223 Sensitivity Cylofold: 0.527 Mastr(seed): 0.050 Positive Predictive Value Cylofold: 0.729 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	53 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.563 Mastr(seed): 0.236 Sensitivity McQFold: 0.489 Mastr(seed): 0.062 Positive Predictive Value McQFold: 0.652 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.561 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.466 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.682 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	9 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.472 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.616 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	51 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.580 Mastr(seed): 0.251 Sensitivity Pknots: 0.526 Mastr(seed): 0.071 Positive Predictive Value Pknots: 0.645 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.635 Mastr(seed): 0.440 Sensitivity RNASampler(seed): 0.484 Mastr(seed): 0.216 Positive Predictive Value RNASampler(seed): 0.837 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	29 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.655 Mastr(seed): 0.367 Sensitivity Alterna: 0.587 Mastr(seed): 0.151 Positive Predictive Value Alterna: 0.737 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.514 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.339 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.784 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.525 Mastr(seed): 0.241 Sensitivity Vsfold4: 0.449 Mastr(seed): 0.065 Positive Predictive Value Vsfold4: 0.618 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.514 Mastr(seed): 0.333 Sensitivity Murlet(seed): 0.315 Mastr(seed): 0.124 Positive Predictive Value Murlet(seed): 0.846 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	52 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.478 Mastr(seed): 0.239 Sensitivity Vsfold5: 0.412 Mastr(seed): 0.064 Positive Predictive Value Vsfold5: 0.559 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.460 Mastr(seed): 0.251 Sensitivity MCFold: 0.478 Mastr(seed): 0.073 Positive Predictive Value MCFold: 0.450 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.548 Mastr(seed): 0.343 Sensitivity RDfolder: 0.455 Mastr(seed): 0.132 Positive Predictive Value RDfolder: 0.671 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.389 Mastr(seed): 0.033 Sensitivity RNAwolf: 0.363 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.426 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	4 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.546 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.366 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.822 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.292 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.300 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.294 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	8 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.558 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.434 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.725 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.092 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.016 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.524 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	60 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.266 Mastr(seed): 0.221 Sensitivity RSpredict(seed): 0.128 Mastr(seed): 0.057 Positive Predictive Value RSpredict(seed): 0.561 Mastr(seed): 0.870 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.306 Carnac(seed): 0.241 Sensitivity Mastr(seed): 0.105 Carnac(seed): 0.058 Positive Predictive Value Mastr(seed): 0.900 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08		? Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.642 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.924 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CMfinder(seed)	0 CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(seed)	1 PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidAlifold(20): 0.662 Sensitivity PETfold_2.0(seed): 0.614 CentroidAlifold(20): 0.474 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidAlifold(20): 0.931 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.775 PETfold_2.0(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.642 PETfold_2.0(seed): 0.642 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.780 PETfold_2.0(seed): 0.769 Sensitivity ContextFold: 0.632 PETfold_2.0(seed): 0.642 Positive Predictive Value ContextFold: 0.968 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MXScarna(seed): 0.682 Sensitivity PETfold_2.0(seed): 0.642 MXScarna(seed): 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 MXScarna(seed): 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNAalifold(20): 0.654 Sensitivity PETfold_2.0(seed): 0.614 RNAalifold(20): 0.491 Positive Predictive Value PETfold_2.0(seed): 0.946 RNAalifold(20): 0.875 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_pre2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_pre2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 IPknot: 0.610 Sensitivity PETfold_2.0(seed): 0.642 IPknot: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 IPknot: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidAlifold(seed): 0.618 Sensitivity PETfold_2.0(seed): 0.642 CentroidAlifold(seed): 0.432 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNASampler(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(seed): 0.946 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 MXScarna(20): 0.741 Sensitivity PETfold_2.0(seed): 0.614 MXScarna(20): 0.614 Positive Predictive Value PETfold_2.0(seed): 0.946 MXScarna(20): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Sfold: 0.673 Sensitivity PETfold_2.0(seed): 0.642 Sfold: 0.537 Positive Predictive Value PETfold_2.0(seed): 0.924 Sfold: 0.850 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(seed): 0.614 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Contrafold: 0.649 Sensitivity PETfold_2.0(seed): 0.642 Contrafold: 0.547 Positive Predictive Value PETfold_2.0(seed): 0.924 Contrafold: 0.776 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RNAalifold(seed): 0.706 Sensitivity PETfold_2.0(seed): 0.684 RNAalifold(seed): 0.500 Positive Predictive Value PETfold_2.0(seed): 0.897 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 HotKnots: 0.682 Sensitivity PETfold_2.0(seed): 0.642 HotKnots: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 HotKnots: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MaxExpect: 0.657 Sensitivity PETfold_2.0(seed): 0.642 MaxExpect: 0.558 Positive Predictive Value PETfold_2.0(seed): 0.924 MaxExpect: 0.779 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidFold: 0.506 Sensitivity PETfold_2.0(seed): 0.642 CentroidFold: 0.421 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidFold: 0.615 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 UNAFold: 0.687 Sensitivity PETfold_2.0(seed): 0.642 UNAFold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 UNAFold: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 PknotsRG: 0.687 Sensitivity PETfold_2.0(seed): 0.642 PknotsRG: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 PknotsRG: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 ProbKnot: 0.675 Sensitivity PETfold_2.0(seed): 0.642 ProbKnot: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 ProbKnot: 0.806 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Murlet(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(seed): 0.946 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAfold: 0.682 Sensitivity PETfold_2.0(seed): 0.642 RNAfold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAfold: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Carnac(20): 0.576 Sensitivity PETfold_2.0(seed): 0.614 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(seed): 0.946 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAshapes: 0.493 Sensitivity PETfold_2.0(seed): 0.642 RNAshapes: 0.411 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAshapes: 0.600 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Fold: 0.665 Sensitivity PETfold_2.0(seed): 0.642 Fold: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 Fold: 0.783 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity TurboFold(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAsubopt: 0.685 Sensitivity PETfold_2.0(seed): 0.642 RNAsubopt: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAsubopt: 0.831 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNASLOpt: 0.625 Sensitivity PETfold_2.0(seed): 0.642 RNASLOpt: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 RNASLOpt: 0.797 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 McQFold: 0.616 Sensitivity PETfold_2.0(seed): 0.642 McQFold: 0.453 Positive Predictive Value PETfold_2.0(seed): 0.924 McQFold: 0.843 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Pknots: 0.607 Sensitivity PETfold_2.0(seed): 0.642 Pknots: 0.516 Positive Predictive Value PETfold_2.0(seed): 0.924 Pknots: 0.721 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Mastr(20): 0.189 Sensitivity PETfold_2.0(seed): 0.614 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold4: 0.167 Sensitivity PETfold_2.0(seed): 0.614 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Murlet(seed): 0.431 Sensitivity PETfold_2.0(seed): 0.684 Murlet(seed): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.897 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold5: 0.156 Sensitivity PETfold_2.0(seed): 0.614 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAwolf: 0.549 Sensitivity PETfold_2.0(seed): 0.642 RNAwolf: 0.484 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAwolf: 0.630 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CMfinder(20): 0.383 Sensitivity PETfold_2.0(seed): 0.614 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.946 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 NanoFolder: 0.243 Sensitivity PETfold_2.0(seed): 0.614 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(seed): 0.946 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity Multilign(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RSpredict(seed): 0.513 Sensitivity PETfold_2.0(seed): 0.684 RSpredict(seed): 0.289 Positive Predictive Value PETfold_2.0(seed): 0.897 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.642 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.924 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
DAFS(20)	0 CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(20)	1 CentroidAlifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.662 PETfold_2.0(20): 0.647 Sensitivity CentroidAlifold(20): 0.474 PETfold_2.0(20): 0.509 Positive Predictive Value CentroidAlifold(20): 0.931 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.760 PETfold_2.0(20): 0.647 Sensitivity ContextFold: 0.579 PETfold_2.0(20): 0.509 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MXScarna(seed): 0.563 Sensitivity PETfold_2.0(20): 0.509 MXScarna(seed): 0.456 Positive Predictive Value PETfold_2.0(20): 0.829 MXScarna(seed): 0.703 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 RNAalifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(20): 0.654 PETfold_2.0(20): 0.647 Sensitivity RNAalifold(20): 0.491 PETfold_2.0(20): 0.509 Positive Predictive Value RNAalifold(20): 0.875 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.647 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(20): 0.509 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.829 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 IPknot: 0.401 Sensitivity PETfold_2.0(20): 0.509 IPknot: 0.298 Positive Predictive Value PETfold_2.0(20): 0.829 IPknot: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidAlifold(seed): 0.484 Sensitivity PETfold_2.0(20): 0.509 CentroidAlifold(seed): 0.281 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidAlifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASampler(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 0.741 PETfold_2.0(20): 0.647 Sensitivity MXScarna(20): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value MXScarna(20): 0.897 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Sfold: 0.514 Sensitivity PETfold_2.0(20): 0.509 Sfold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(20): 0.509 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Contrafold: 0.482 Sensitivity PETfold_2.0(20): 0.509 Contrafold: 0.386 Positive Predictive Value PETfold_2.0(20): 0.829 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 HotKnots: 0.541 Sensitivity PETfold_2.0(20): 0.509 HotKnots: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MaxExpect: 0.498 Sensitivity PETfold_2.0(20): 0.509 MaxExpect: 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidFold: 0.467 Sensitivity PETfold_2.0(20): 0.509 CentroidFold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 UNAFold: 0.549 Sensitivity PETfold_2.0(20): 0.509 UNAFold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 UNAFold: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.647 PknotsRG: 0.549 Sensitivity PETfold_2.0(20): 0.509 PknotsRG: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 PknotsRG: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 ProbKnot: 0.527 Sensitivity PETfold_2.0(20): 0.509 ProbKnot: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Murlet(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAfold: 0.541 Sensitivity PETfold_2.0(20): 0.509 RNAfold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 RNAfold: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Carnac(20): 0.576 Sensitivity PETfold_2.0(20): 0.509 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(20): 0.829 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAshapes: 0.199 Sensitivity PETfold_2.0(20): 0.509 RNAshapes: 0.158 Positive Predictive Value PETfold_2.0(20): 0.829 RNAshapes: 0.265 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Fold: 0.513 Sensitivity PETfold_2.0(20): 0.509 Fold: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 Fold: 0.632 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAsubopt: 0.542 Sensitivity PETfold_2.0(20): 0.509 RNAsubopt: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASLOpt: 0.456 Sensitivity PETfold_2.0(20): 0.509 RNASLOpt: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 RNASLOpt: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 McQFold: 0.491 Sensitivity PETfold_2.0(20): 0.509 McQFold: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 McQFold: 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Pknots: 0.410 Sensitivity PETfold_2.0(20): 0.509 Pknots: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 Pknots: 0.514 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(20): 0.189 Sensitivity PETfold_2.0(20): 0.509 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold4: 0.167 Sensitivity PETfold_2.0(20): 0.509 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold5: 0.156 Sensitivity PETfold_2.0(20): 0.509 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAwolf: 0.431 Sensitivity PETfold_2.0(20): 0.509 RNAwolf: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 RNAwolf: 0.512 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CMfinder(20): 0.383 Sensitivity PETfold_2.0(20): 0.509 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(20): 0.829 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.647 NanoFolder: 0.243 Sensitivity PETfold_2.0(20): 0.509 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(20): 0.829 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
DAFS(seed)	0 DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A

Matthews Correlation Coefficients (MCC) plotted for all methods in a ranking. MCCs were calculated by taking into account all reference and predicted RNA structures by a given method in the entire ranking. The plot includes only methods for which at least 40% of comparisons with other methods is valid (i.e. at least 40% of the comparisons were based on more than 10 predictions for common targets).

All RNAs from the PDB datasetextended base pair definition

Summary of pairwise comparisons

Detailed results of pairwise comparisons between methods

All RNAs from the PDB dataset
extended base pair definition