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: Oct. 2, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Number of RNA sequences: 121
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 Oct. 2, 2012.

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: 21) 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

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 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 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Tested since	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	MXScarna(seed)	no	2009-06-15	38	2	1	12	44	44
2	CentroidFold	yes	2009-08-01	37	7	1	8	106	106
3	CentroidAlifold(20)	yes	2009-07-01	36	0	0	17	26	26
4	RNAalifold(20)	no	2009-02-18	34	2	0	17	28	28
5	RNASampler(20)	no	2009-02-18	32	3	1	17	28	28
6	Sfold	no	2009-02-18	32	11	2	8	121	121
7	MXScarna(20)	no	2009-02-18	31	4	1	17	28	28
8	Contrafold	yes	2009-02-18	31	11	3	8	121	121
8	Fold	no	2010-03-15	31	11	3	8	82	82
10	HotKnots	no	2009-02-18	29	13	3	8	121	118
11	CentroidHomfold‑LAST	yes	2011-05-11	28	1	3	21	45	44
12	IPknot	yes	2011-07-01	28	2	2	21	38	38
13	UNAFold	no	2009-02-18	28	14	3	8	121	121
13	MaxExpect	yes	2009-10-15	28	14	3	8	100	99
15	ContextFold	yes	2011-11-15	27	0	0	26	30	30
16	RNAshapes	no	2009-02-18	26	16	3	8	121	118
17	RNAfold	no	2009-02-18	25	17	3	8	121	121
18	PknotsRG	no	2009-02-18	24	18	3	8	121	121
19	CentroidAlifold(seed)	yes	2009-07-01	23	7	11	12	43	43
20	ProbKnot	yes	2010-08-10	22	20	2	9	74	74
21	Murlet(20)	yes	2009-02-18	19	12	5	17	28	28
22	Carnac(20)	no	2009-02-18	19	13	4	17	28	28
23	Afold	no	2009-02-18	19	20	4	10	121	95
24	RNAsubopt	no	2009-02-18	18	24	3	8	121	118
25	Cylofold	no	2010-06-08	15	24	3	11	76	63
26	McQFold	yes	2009-02-18	15	26	4	8	121	120
27	RNAalifold(seed)	no	2009-02-18	14	19	3	17	45	29
28	Pknots	no	2009-02-18	14	28	3	8	121	116
29	Alterna	no	2009-02-18	13	28	1	11	121	89
30	RNASampler(seed)	no	2009-02-18	12	12	2	27	45	17
31	CRWrnafold	yes	2011-08-23	11	12	4	26	36	32
32	RSpredict(20)	no	2009-06-03	11	24	1	17	27	27
33	Mastr(20)	yes	2009-02-18	10	24	2	17	28	28
34	Vsfold4	no	2009-02-18	9	35	1	8	121	118
35	RNASLOpt	no	2011-11-01	8	16	3	26	30	30
36	Multilign(20)	no	2011-03-01	6	20	2	25	10	10
37	RNAwolf	yes	2011-07-01	6	26	0	21	38	38
38	Murlet(seed)	yes	2009-02-18	6	27	3	17	45	26
39	MCFold	yes	2009-02-18	5	36	2	10	121	109
40	Vsfold5	no	2009-02-18	5	39	1	8	121	117
41	RDfolder	no	2009-02-18	4	37	1	11	121	92
42	RSpredict(seed)	no	2009-06-03	3	38	0	12	44	44
43	PPfold(seed)	yes	2011-04-18	1	22	0	30	12	11
44	NanoFolder	yes	2011-11-17	1	24	0	28	20	17
45	Mastr(seed)	yes	2009-02-18	1	40	0	12	45	45
46	Carnac(seed)	no	2009-02-18	0	36	0	17	45	30
N/A	Multilign(seed)	no	2011-03-01	0	0	0	53	13	5
N/A	TurboFold(seed)	no	2011-04-20	0	0	0	53	12	9
N/A	TurboFold(20)	no	2011-04-20	0	0	0	53	9	9
N/A	PPfold(20)	yes	2011-04-18	0	0	0	53	9	9
N/A	PETfold_pre2.0(seed)	no	2011-11-03	0	0	0	53	8	8
N/A	PETfold_pre2.0(20)	no	2011-11-03	0	0	0	53	5	5
N/A	CMfinder(seed)	yes	2012-09-01	0	0	0	53	0	0
N/A	CMfinder(20)	yes	2012-09-01	0	0	0	53	0	0

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.


MXScarna(seed)		+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.671 CentroidFold: 0.625 Sensitivity MXScarna(seed): 0.560 CentroidFold: 0.545 Positive Predictive Value MXScarna(seed): 0.807 CentroidFold: 0.719 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MXScarna(seed): 0.664 Sensitivity CentroidAlifold(20): 0.520 MXScarna(seed): 0.552 Positive Predictive Value CentroidAlifold(20): 0.892 MXScarna(seed): 0.802 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RNAalifold(20): 0.642 Sensitivity MXScarna(seed): 0.556 RNAalifold(20): 0.491 Positive Predictive Value MXScarna(seed): 0.805 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RNASampler(20): 0.640 Sensitivity MXScarna(seed): 0.556 RNASampler(20): 0.489 Positive Predictive Value MXScarna(seed): 0.805 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.673 Sfold: 0.608 Sensitivity MXScarna(seed): 0.562 Sfold: 0.525 Positive Predictive Value MXScarna(seed): 0.809 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 MXScarna(20): 0.634 Sensitivity MXScarna(seed): 0.556 MXScarna(20): 0.530 Positive Predictive Value MXScarna(seed): 0.805 MXScarna(20): 0.761 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.673 Contrafold: 0.599 Sensitivity MXScarna(seed): 0.562 Contrafold: 0.544 Positive Predictive Value MXScarna(seed): 0.809 Contrafold: 0.664 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.665 Fold: 0.625 Sensitivity MXScarna(seed): 0.555 Fold: 0.569 Positive Predictive Value MXScarna(seed): 0.801 Fold: 0.690 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.673 HotKnots: 0.601 Sensitivity MXScarna(seed): 0.562 HotKnots: 0.549 Positive Predictive Value MXScarna(seed): 0.809 HotKnots: 0.663 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 MXScarna(seed): 0.621 Sensitivity CentroidHomfold‑LAST: 0.501 MXScarna(seed): 0.496 Positive Predictive Value CentroidHomfold‑LAST: 0.808 MXScarna(seed): 0.782 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.54564345795e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.624 IPknot: 0.590 Sensitivity MXScarna(seed): 0.493 IPknot: 0.471 Positive Predictive Value MXScarna(seed): 0.796 IPknot: 0.747 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.667 MaxExpect: 0.605 Sensitivity MXScarna(seed): 0.557 MaxExpect: 0.543 Positive Predictive Value MXScarna(seed): 0.801 MaxExpect: 0.677 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.673 UNAFold: 0.599 Sensitivity MXScarna(seed): 0.562 UNAFold: 0.540 Positive Predictive Value MXScarna(seed): 0.809 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.616 MXScarna(seed): 0.586 Sensitivity ContextFold: 0.476 MXScarna(seed): 0.457 Positive Predictive Value ContextFold: 0.801 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAshapes: 0.597 Sensitivity MXScarna(seed): 0.562 RNAshapes: 0.537 Positive Predictive Value MXScarna(seed): 0.809 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAfold: 0.603 Sensitivity MXScarna(seed): 0.562 RNAfold: 0.548 Positive Predictive Value MXScarna(seed): 0.809 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.673 PknotsRG: 0.602 Sensitivity MXScarna(seed): 0.562 PknotsRG: 0.549 Positive Predictive Value MXScarna(seed): 0.809 PknotsRG: 0.665 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.671 CentroidAlifold(seed): 0.605 Sensitivity MXScarna(seed): 0.560 CentroidAlifold(seed): 0.419 Positive Predictive Value MXScarna(seed): 0.807 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.653 ProbKnot: 0.570 Sensitivity MXScarna(seed): 0.541 ProbKnot: 0.529 Positive Predictive Value MXScarna(seed): 0.791 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Murlet(20): 0.582 Sensitivity MXScarna(seed): 0.556 Murlet(20): 0.425 Positive Predictive Value MXScarna(seed): 0.805 Murlet(20): 0.800 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Carnac(20): 0.586 Sensitivity MXScarna(seed): 0.556 Carnac(20): 0.377 Positive Predictive Value MXScarna(seed): 0.805 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.664 Afold: 0.570 Sensitivity MXScarna(seed): 0.554 Afold: 0.534 Positive Predictive Value MXScarna(seed): 0.799 Afold: 0.613 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAsubopt: 0.570 Sensitivity MXScarna(seed): 0.562 RNAsubopt: 0.521 Positive Predictive Value MXScarna(seed): 0.809 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.676 Cylofold: 0.640 Sensitivity MXScarna(seed): 0.565 Cylofold: 0.553 Positive Predictive Value MXScarna(seed): 0.814 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.32337795675e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.673 McQFold: 0.565 Sensitivity MXScarna(seed): 0.562 McQFold: 0.500 Positive Predictive Value MXScarna(seed): 0.809 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 RNAalifold(seed): 0.593 Sensitivity MXScarna(seed): 0.533 RNAalifold(seed): 0.397 Positive Predictive Value MXScarna(seed): 0.788 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.687 Pknots: 0.615 Sensitivity MXScarna(seed): 0.577 Pknots: 0.562 Positive Predictive Value MXScarna(seed): 0.823 Pknots: 0.679 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-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: 5.19332990918e-08	= RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 MXScarna(seed): 0.672 Sensitivity RNASampler(seed): 0.535 MXScarna(seed): 0.566 Positive Predictive Value RNASampler(seed): 0.851 MXScarna(seed): 0.804 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0250258449044	? 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 RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RSpredict(20): 0.547 Sensitivity MXScarna(seed): 0.556 RSpredict(20): 0.428 Positive Predictive Value MXScarna(seed): 0.805 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Mastr(20): 0.527 Sensitivity MXScarna(seed): 0.556 Mastr(20): 0.348 Positive Predictive Value MXScarna(seed): 0.805 Mastr(20): 0.803 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.673 Vsfold4: 0.517 Sensitivity MXScarna(seed): 0.562 Vsfold4: 0.445 Positive Predictive Value MXScarna(seed): 0.809 Vsfold4: 0.605 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.586 RNASLOpt: 0.474 Sensitivity MXScarna(seed): 0.457 RNASLOpt: 0.374 Positive Predictive Value MXScarna(seed): 0.758 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.639 Multilign(20): 0.521 Sensitivity MXScarna(seed): 0.521 Multilign(20): 0.428 Positive Predictive Value MXScarna(seed): 0.790 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.624 RNAwolf: 0.414 Sensitivity MXScarna(seed): 0.493 RNAwolf: 0.375 Positive Predictive Value MXScarna(seed): 0.796 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.671 Murlet(seed): 0.539 Sensitivity MXScarna(seed): 0.561 Murlet(seed): 0.337 Positive Predictive Value MXScarna(seed): 0.808 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.692 MCFold: 0.502 Sensitivity MXScarna(seed): 0.585 MCFold: 0.526 Positive Predictive Value MXScarna(seed): 0.824 MCFold: 0.487 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.673 Vsfold5: 0.491 Sensitivity MXScarna(seed): 0.562 Vsfold5: 0.426 Positive Predictive Value MXScarna(seed): 0.809 Vsfold5: 0.570 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.714 RDfolder: 0.556 Sensitivity MXScarna(seed): 0.598 RDfolder: 0.462 Positive Predictive Value MXScarna(seed): 0.858 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.673 RSpredict(seed): 0.314 Sensitivity MXScarna(seed): 0.562 RSpredict(seed): 0.161 Positive Predictive Value MXScarna(seed): 0.809 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.624 PPfold(seed): 0.102 Sensitivity MXScarna(seed): 0.493 PPfold(seed): 0.020 Positive Predictive Value MXScarna(seed): 0.796 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	? MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.594 NanoFolder: 0.346 Sensitivity MXScarna(seed): 0.468 NanoFolder: 0.353 Positive Predictive Value MXScarna(seed): 0.759 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.673 Mastr(seed): 0.263 Sensitivity MXScarna(seed): 0.562 Mastr(seed): 0.077 Positive Predictive Value MXScarna(seed): 0.809 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 44 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	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 MXScarna(seed): 0.575 Sensitivity Multilign(seed): 0.475 MXScarna(seed): 0.475 Positive Predictive Value Multilign(seed): 0.750 MXScarna(seed): 0.708 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MXScarna(seed): 0.586 Sensitivity PETfold_pre2.0(seed): 0.551 MXScarna(seed): 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.634 TurboFold(20): 0.620 Sensitivity MXScarna(seed): 0.514 TurboFold(20): 0.500 Positive Predictive Value MXScarna(seed): 0.788 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(seed): 0.593 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(seed): 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(seed): 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.573 TurboFold(seed): 0.550 Sensitivity MXScarna(seed): 0.459 TurboFold(seed): 0.456 Positive Predictive Value MXScarna(seed): 0.722 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(seed): 0.634 Sensitivity PPfold(20): 0.514 MXScarna(seed): 0.514 Positive Predictive Value PPfold(20): 0.861 MXScarna(seed): 0.788 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.678 Carnac(seed): 0.260 Sensitivity MXScarna(seed): 0.575 Carnac(seed): 0.068 Positive Predictive Value MXScarna(seed): 0.803 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	43 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.671 CentroidFold: 0.625 Sensitivity MXScarna(seed): 0.560 CentroidFold: 0.545 Positive Predictive Value MXScarna(seed): 0.807 CentroidFold: 0.719 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 CentroidFold: 0.597 Sensitivity CentroidAlifold(20): 0.520 CentroidFold: 0.506 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	- RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.642 CentroidFold: 0.597 Sensitivity RNAalifold(20): 0.492 CentroidFold: 0.506 Positive Predictive Value RNAalifold(20): 0.842 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.636 CentroidFold: 0.597 Sensitivity RNASampler(20): 0.484 CentroidFold: 0.506 Positive Predictive Value RNASampler(20): 0.840 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.577 Sfold: 0.548 Sensitivity CentroidFold: 0.493 Sfold: 0.470 Positive Predictive Value CentroidFold: 0.676 Sfold: 0.641 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.630 CentroidFold: 0.597 Sensitivity MXScarna(20): 0.526 CentroidFold: 0.506 Positive Predictive Value MXScarna(20): 0.758 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.577 Contrafold: 0.574 Sensitivity CentroidFold: 0.493 Contrafold: 0.516 Positive Predictive Value CentroidFold: 0.676 Contrafold: 0.639 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 9.17559933998e-05	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.693 Fold: 0.679 Sensitivity CentroidFold: 0.608 Fold: 0.618 Positive Predictive Value CentroidFold: 0.793 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.676 HotKnots: 0.662 Sensitivity CentroidFold: 0.591 HotKnots: 0.603 Positive Predictive Value CentroidFold: 0.777 HotKnots: 0.731 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 CentroidFold: 0.667 Sensitivity CentroidHomfold‑LAST: 0.515 CentroidFold: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.873 CentroidFold: 0.792 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 0.716668360784	- IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.675 CentroidFold: 0.665 Sensitivity IPknot: 0.573 CentroidFold: 0.565 Positive Predictive Value IPknot: 0.801 CentroidFold: 0.789 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.631 MaxExpect: 0.617 Sensitivity CentroidFold: 0.530 MaxExpect: 0.540 Positive Predictive Value CentroidFold: 0.754 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.577 UNAFold: 0.526 Sensitivity CentroidFold: 0.493 UNAFold: 0.476 Positive Predictive Value CentroidFold: 0.676 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.705 CentroidFold: 0.654 Sensitivity ContextFold: 0.594 CentroidFold: 0.556 Positive Predictive Value ContextFold: 0.843 CentroidFold: 0.775 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.676 RNAshapes: 0.650 Sensitivity CentroidFold: 0.591 RNAshapes: 0.584 Positive Predictive Value CentroidFold: 0.777 RNAshapes: 0.728 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.577 RNAfold: 0.519 Sensitivity CentroidFold: 0.493 RNAfold: 0.475 Positive Predictive Value CentroidFold: 0.676 RNAfold: 0.568 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.577 PknotsRG: 0.510 Sensitivity CentroidFold: 0.493 PknotsRG: 0.468 Positive Predictive Value CentroidFold: 0.676 PknotsRG: 0.558 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.625 CentroidAlifold(seed): 0.605 Sensitivity CentroidFold: 0.545 CentroidAlifold(seed): 0.419 Positive Predictive Value CentroidFold: 0.719 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.674 ProbKnot: 0.646 Sensitivity CentroidFold: 0.590 ProbKnot: 0.597 Positive Predictive Value CentroidFold: 0.774 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.597 Murlet(20): 0.581 Sensitivity CentroidFold: 0.506 Murlet(20): 0.425 Positive Predictive Value CentroidFold: 0.707 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.18973841657e-07	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.597 Carnac(20): 0.584 Sensitivity CentroidFold: 0.506 Carnac(20): 0.375 Positive Predictive Value CentroidFold: 0.707 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.80284942886e-07	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.565 Afold: 0.500 Sensitivity CentroidFold: 0.485 Afold: 0.463 Positive Predictive Value CentroidFold: 0.658 Afold: 0.541 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.676 RNAsubopt: 0.638 Sensitivity CentroidFold: 0.591 RNAsubopt: 0.580 Positive Predictive Value CentroidFold: 0.777 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.711 Cylofold: 0.648 Sensitivity CentroidFold: 0.615 Cylofold: 0.559 Positive Predictive Value CentroidFold: 0.827 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.576 McQFold: 0.472 Sensitivity CentroidFold: 0.492 McQFold: 0.365 Positive Predictive Value CentroidFold: 0.674 McQFold: 0.612 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.628 RNAalifold(seed): 0.593 Sensitivity CentroidFold: 0.547 RNAalifold(seed): 0.399 Positive Predictive Value CentroidFold: 0.725 RNAalifold(seed): 0.886 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.698 Pknots: 0.637 Sensitivity CentroidFold: 0.608 Pknots: 0.580 Positive Predictive Value CentroidFold: 0.807 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-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 RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.707 RNASampler(seed): 0.665 Sensitivity CentroidFold: 0.626 RNASampler(seed): 0.525 Positive Predictive Value CentroidFold: 0.804 RNASampler(seed): 0.846 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.26346675981e-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 RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.597 RSpredict(20): 0.543 Sensitivity CentroidFold: 0.506 RSpredict(20): 0.425 Positive Predictive Value CentroidFold: 0.707 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.597 Mastr(20): 0.521 Sensitivity CentroidFold: 0.506 Mastr(20): 0.342 Positive Predictive Value CentroidFold: 0.707 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.676 Vsfold4: 0.563 Sensitivity CentroidFold: 0.591 Vsfold4: 0.484 Positive Predictive Value CentroidFold: 0.777 Vsfold4: 0.661 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.654 RNASLOpt: 0.591 Sensitivity CentroidFold: 0.556 RNASLOpt: 0.498 Positive Predictive Value CentroidFold: 0.775 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.548 Multilign(20): 0.521 Sensitivity CentroidFold: 0.452 Multilign(20): 0.428 Positive Predictive Value CentroidFold: 0.673 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.665 RNAwolf: 0.512 Sensitivity CentroidFold: 0.565 RNAwolf: 0.479 Positive Predictive Value CentroidFold: 0.789 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.675 Murlet(seed): 0.540 Sensitivity CentroidFold: 0.578 Murlet(seed): 0.338 Positive Predictive Value CentroidFold: 0.794 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.703 MCFold: 0.566 Sensitivity CentroidFold: 0.615 MCFold: 0.588 Positive Predictive Value CentroidFold: 0.809 MCFold: 0.553 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.675 Vsfold5: 0.526 Sensitivity CentroidFold: 0.590 Vsfold5: 0.457 Positive Predictive Value CentroidFold: 0.777 Vsfold5: 0.611 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.733 RDfolder: 0.581 Sensitivity CentroidFold: 0.638 RDfolder: 0.483 Positive Predictive Value CentroidFold: 0.850 RDfolder: 0.708 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.625 RSpredict(seed): 0.308 Sensitivity CentroidFold: 0.545 RSpredict(seed): 0.156 Positive Predictive Value CentroidFold: 0.719 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.578 PPfold(seed): 0.102 Sensitivity CentroidFold: 0.465 PPfold(seed): 0.020 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.663 NanoFolder: 0.490 Sensitivity CentroidFold: 0.567 NanoFolder: 0.495 Positive Predictive Value CentroidFold: 0.782 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Mastr(seed): 0.264 Sensitivity CentroidFold: 0.545 Mastr(seed): 0.078 Positive Predictive Value CentroidFold: 0.719 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 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	? CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Multilign(seed): 0.593 Sensitivity CentroidFold: 0.500 Multilign(seed): 0.475 Positive Predictive Value CentroidFold: 0.790 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidFold: 0.540 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidFold: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.620 CentroidFold: 0.603 Sensitivity TurboFold(20): 0.500 CentroidFold: 0.500 Positive Predictive Value TurboFold(20): 0.775 CentroidFold: 0.732 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidFold: 0.517 Sensitivity PETfold_pre2.0(20): 0.497 CentroidFold: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.585 TurboFold(seed): 0.550 Sensitivity CentroidFold: 0.481 TurboFold(seed): 0.456 Positive Predictive Value CentroidFold: 0.720 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.663 CentroidFold: 0.603 Sensitivity PPfold(20): 0.514 CentroidFold: 0.500 Positive Predictive Value PPfold(20): 0.861 CentroidFold: 0.732 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.668 Carnac(seed): 0.240 Sensitivity CentroidFold: 0.578 Carnac(seed): 0.058 Positive Predictive Value CentroidFold: 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08
CentroidAlifold(20)	26 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MXScarna(seed): 0.664 Sensitivity CentroidAlifold(20): 0.520 MXScarna(seed): 0.552 Positive Predictive Value CentroidAlifold(20): 0.892 MXScarna(seed): 0.802 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 CentroidFold: 0.597 Sensitivity CentroidAlifold(20): 0.520 CentroidFold: 0.506 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAalifold(20): 0.642 Sensitivity CentroidAlifold(20): 0.520 RNAalifold(20): 0.492 Positive Predictive Value CentroidAlifold(20): 0.892 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNASampler(20): 0.636 Sensitivity CentroidAlifold(20): 0.520 RNASampler(20): 0.484 Positive Predictive Value CentroidAlifold(20): 0.892 RNASampler(20): 0.840 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Sfold: 0.589 Sensitivity CentroidAlifold(20): 0.520 Sfold: 0.495 Positive Predictive Value CentroidAlifold(20): 0.892 Sfold: 0.706 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MXScarna(20): 0.630 Sensitivity CentroidAlifold(20): 0.520 MXScarna(20): 0.526 Positive Predictive Value CentroidAlifold(20): 0.892 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Contrafold: 0.552 Sensitivity CentroidAlifold(20): 0.520 Contrafold: 0.490 Positive Predictive Value CentroidAlifold(20): 0.892 Contrafold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.671 Fold: 0.610 Sensitivity CentroidAlifold(20): 0.500 Fold: 0.542 Positive Predictive Value CentroidAlifold(20): 0.904 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.680 HotKnots: 0.577 Sensitivity CentroidAlifold(20): 0.520 HotKnots: 0.517 Positive Predictive Value CentroidAlifold(20): 0.892 HotKnots: 0.648 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	? CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.684 CentroidHomfold‑LAST: 0.654 Sensitivity CentroidAlifold(20): 0.517 CentroidHomfold‑LAST: 0.524 Positive Predictive Value CentroidAlifold(20): 0.909 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 IPknot: 0.571 Sensitivity CentroidAlifold(20): 0.515 IPknot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.933 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MaxExpect: 0.588 Sensitivity CentroidAlifold(20): 0.520 MaxExpect: 0.516 Positive Predictive Value CentroidAlifold(20): 0.892 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 UNAFold: 0.585 Sensitivity CentroidAlifold(20): 0.520 UNAFold: 0.515 Positive Predictive Value CentroidAlifold(20): 0.892 UNAFold: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.650 ContextFold: 0.579 Sensitivity CentroidAlifold(20): 0.473 ContextFold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.898 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAshapes: 0.582 Sensitivity CentroidAlifold(20): 0.520 RNAshapes: 0.512 Positive Predictive Value CentroidAlifold(20): 0.892 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAfold: 0.566 Sensitivity CentroidAlifold(20): 0.520 RNAfold: 0.505 Positive Predictive Value CentroidAlifold(20): 0.892 RNAfold: 0.638 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.680 PknotsRG: 0.576 Sensitivity CentroidAlifold(20): 0.520 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(20): 0.892 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 CentroidAlifold(seed): 0.629 Sensitivity CentroidAlifold(20): 0.520 CentroidAlifold(seed): 0.430 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.671 ProbKnot: 0.586 Sensitivity CentroidAlifold(20): 0.500 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(20): 0.904 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Murlet(20): 0.581 Sensitivity CentroidAlifold(20): 0.520 Murlet(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.892 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Carnac(20): 0.584 Sensitivity CentroidAlifold(20): 0.520 Carnac(20): 0.375 Positive Predictive Value CentroidAlifold(20): 0.892 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.641 Afold: 0.513 Sensitivity CentroidAlifold(20): 0.484 Afold: 0.472 Positive Predictive Value CentroidAlifold(20): 0.852 Afold: 0.563 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAsubopt: 0.560 Sensitivity CentroidAlifold(20): 0.520 RNAsubopt: 0.503 Positive Predictive Value CentroidAlifold(20): 0.892 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.703 Cylofold: 0.608 Sensitivity CentroidAlifold(20): 0.536 Cylofold: 0.523 Positive Predictive Value CentroidAlifold(20): 0.926 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 McQFold: 0.531 Sensitivity CentroidAlifold(20): 0.520 McQFold: 0.463 Positive Predictive Value CentroidAlifold(20): 0.892 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.638 RNAalifold(seed): 0.573 Sensitivity CentroidAlifold(20): 0.454 RNAalifold(seed): 0.357 Positive Predictive Value CentroidAlifold(20): 0.900 RNAalifold(seed): 0.922 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Pknots: 0.542 Sensitivity CentroidAlifold(20): 0.540 Pknots: 0.495 Positive Predictive Value CentroidAlifold(20): 0.893 Pknots: 0.598 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-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: 9.16590079822e-09	? CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.586 RNASampler(seed): 0.560 Sensitivity CentroidAlifold(20): 0.421 RNASampler(seed): 0.421 Positive Predictive Value CentroidAlifold(20): 0.821 RNASampler(seed): 0.750 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RSpredict(20): 0.543 Sensitivity CentroidAlifold(20): 0.520 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.892 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Mastr(20): 0.521 Sensitivity CentroidAlifold(20): 0.520 Mastr(20): 0.342 Positive Predictive Value CentroidAlifold(20): 0.892 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Vsfold4: 0.452 Sensitivity CentroidAlifold(20): 0.520 Vsfold4: 0.382 Positive Predictive Value CentroidAlifold(20): 0.892 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.650 RNASLOpt: 0.467 Sensitivity CentroidAlifold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.898 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.657 Multilign(20): 0.521 Sensitivity CentroidAlifold(20): 0.476 Multilign(20): 0.428 Positive Predictive Value CentroidAlifold(20): 0.913 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.03233993685e-09	? CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.691 RNAwolf: 0.364 Sensitivity CentroidAlifold(20): 0.515 RNAwolf: 0.333 Positive Predictive Value CentroidAlifold(20): 0.933 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 Murlet(seed): 0.490 Sensitivity CentroidAlifold(20): 0.470 Murlet(seed): 0.269 Positive Predictive Value CentroidAlifold(20): 0.904 Murlet(seed): 0.899 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.690 MCFold: 0.414 Sensitivity CentroidAlifold(20): 0.539 MCFold: 0.438 Positive Predictive Value CentroidAlifold(20): 0.888 MCFold: 0.399 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Vsfold5: 0.418 Sensitivity CentroidAlifold(20): 0.520 Vsfold5: 0.358 Positive Predictive Value CentroidAlifold(20): 0.892 Vsfold5: 0.493 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.742 RDfolder: 0.517 Sensitivity CentroidAlifold(20): 0.588 RDfolder: 0.419 Positive Predictive Value CentroidAlifold(20): 0.941 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RSpredict(seed): 0.237 Sensitivity CentroidAlifold(20): 0.520 RSpredict(seed): 0.103 Positive Predictive Value CentroidAlifold(20): 0.892 RSpredict(seed): 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(seed): 0.026 Sensitivity CentroidAlifold(20): 0.515 PPfold(seed): 0.004 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.646 NanoFolder: 0.316 Sensitivity CentroidAlifold(20): 0.473 NanoFolder: 0.324 Positive Predictive Value CentroidAlifold(20): 0.886 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.520 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.892 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 26 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	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.707 Multilign(seed): 0.678 Sensitivity CentroidAlifold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value CentroidAlifold(20): 0.926 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 CentroidAlifold(20): 0.650 Sensitivity PETfold_pre2.0(seed): 0.557 CentroidAlifold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.898 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 TurboFold(20): 0.620 Sensitivity CentroidAlifold(20): 0.517 TurboFold(20): 0.500 Positive Predictive Value CentroidAlifold(20): 0.909 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 PETfold_pre2.0(20): 0.625 Sensitivity CentroidAlifold(20): 0.473 PETfold_pre2.0(20): 0.497 Positive Predictive Value CentroidAlifold(20): 0.898 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.664 TurboFold(seed): 0.595 Sensitivity CentroidAlifold(20): 0.494 TurboFold(seed): 0.490 Positive Predictive Value CentroidAlifold(20): 0.897 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 PPfold(20): 0.663 Sensitivity CentroidAlifold(20): 0.517 PPfold(20): 0.514 Positive Predictive Value CentroidAlifold(20): 0.909 PPfold(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.671 Carnac(seed): 0.160 Sensitivity CentroidAlifold(20): 0.510 Carnac(seed): 0.026 Positive Predictive Value CentroidAlifold(20): 0.887 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08
RNAalifold(20)	27 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RNAalifold(20): 0.642 Sensitivity MXScarna(seed): 0.556 RNAalifold(20): 0.491 Positive Predictive Value MXScarna(seed): 0.805 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.642 CentroidFold: 0.597 Sensitivity RNAalifold(20): 0.492 CentroidFold: 0.506 Positive Predictive Value RNAalifold(20): 0.842 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAalifold(20): 0.642 Sensitivity CentroidAlifold(20): 0.520 RNAalifold(20): 0.492 Positive Predictive Value CentroidAlifold(20): 0.892 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08		+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 RNASampler(20): 0.634 Sensitivity RNAalifold(20): 0.491 RNASampler(20): 0.477 Positive Predictive Value RNAalifold(20): 0.849 RNASampler(20): 0.844 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.644 Sfold: 0.590 Sensitivity RNAalifold(20): 0.491 Sfold: 0.493 Positive Predictive Value RNAalifold(20): 0.849 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 MXScarna(20): 0.628 Sensitivity RNAalifold(20): 0.491 MXScarna(20): 0.523 Positive Predictive Value RNAalifold(20): 0.849 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.644 Contrafold: 0.544 Sensitivity RNAalifold(20): 0.491 Contrafold: 0.481 Positive Predictive Value RNAalifold(20): 0.849 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.626 Fold: 0.610 Sensitivity RNAalifold(20): 0.468 Fold: 0.542 Positive Predictive Value RNAalifold(20): 0.841 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.644 HotKnots: 0.577 Sensitivity RNAalifold(20): 0.491 HotKnots: 0.514 Positive Predictive Value RNAalifold(20): 0.849 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RNAalifold(20): 0.619 Sensitivity CentroidHomfold‑LAST: 0.524 RNAalifold(20): 0.483 Positive Predictive Value CentroidHomfold‑LAST: 0.822 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.627 IPknot: 0.571 Sensitivity RNAalifold(20): 0.481 IPknot: 0.463 Positive Predictive Value RNAalifold(20): 0.823 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.642 MaxExpect: 0.588 Sensitivity RNAalifold(20): 0.492 MaxExpect: 0.516 Positive Predictive Value RNAalifold(20): 0.842 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.644 UNAFold: 0.585 Sensitivity RNAalifold(20): 0.491 UNAFold: 0.512 Positive Predictive Value RNAalifold(20): 0.849 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.579 RNAalifold(20): 0.553 Sensitivity ContextFold: 0.443 RNAalifold(20): 0.407 Positive Predictive Value ContextFold: 0.763 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAshapes: 0.577 Sensitivity RNAalifold(20): 0.491 RNAshapes: 0.506 Positive Predictive Value RNAalifold(20): 0.849 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAfold: 0.567 Sensitivity RNAalifold(20): 0.491 RNAfold: 0.503 Positive Predictive Value RNAalifold(20): 0.849 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.644 PknotsRG: 0.579 Sensitivity RNAalifold(20): 0.491 PknotsRG: 0.516 Positive Predictive Value RNAalifold(20): 0.849 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 CentroidAlifold(seed): 0.629 Sensitivity RNAalifold(20): 0.492 CentroidAlifold(seed): 0.430 Positive Predictive Value RNAalifold(20): 0.842 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.87980998248e-07	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.626 ProbKnot: 0.586 Sensitivity RNAalifold(20): 0.468 ProbKnot: 0.529 Positive Predictive Value RNAalifold(20): 0.841 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Murlet(20): 0.582 Sensitivity RNAalifold(20): 0.491 Murlet(20): 0.423 Positive Predictive Value RNAalifold(20): 0.849 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Carnac(20): 0.582 Sensitivity RNAalifold(20): 0.491 Carnac(20): 0.371 Positive Predictive Value RNAalifold(20): 0.849 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.597 Afold: 0.518 Sensitivity RNAalifold(20): 0.451 Afold: 0.469 Positive Predictive Value RNAalifold(20): 0.793 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAsubopt: 0.550 Sensitivity RNAalifold(20): 0.491 RNAsubopt: 0.492 Positive Predictive Value RNAalifold(20): 0.849 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.668 Cylofold: 0.608 Sensitivity RNAalifold(20): 0.509 Cylofold: 0.523 Positive Predictive Value RNAalifold(20): 0.880 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.644 McQFold: 0.524 Sensitivity RNAalifold(20): 0.491 McQFold: 0.454 Positive Predictive Value RNAalifold(20): 0.849 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.585 RNAalifold(seed): 0.572 Sensitivity RNAalifold(20): 0.420 RNAalifold(seed): 0.356 Positive Predictive Value RNAalifold(20): 0.818 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54600035591e-07	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.658 Pknots: 0.530 Sensitivity RNAalifold(20): 0.511 Pknots: 0.483 Positive Predictive Value RNAalifold(20): 0.852 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ 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: 2.10198558684e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RNAalifold(20): 0.514 Sensitivity RNASampler(seed): 0.444 RNAalifold(20): 0.410 Positive Predictive Value RNASampler(seed): 0.768 RNAalifold(20): 0.649 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(20): 0.547 Sensitivity RNAalifold(20): 0.491 RSpredict(20): 0.428 Positive Predictive Value RNAalifold(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Mastr(20): 0.525 Sensitivity RNAalifold(20): 0.491 Mastr(20): 0.346 Positive Predictive Value RNAalifold(20): 0.849 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.644 Vsfold4: 0.450 Sensitivity RNAalifold(20): 0.491 Vsfold4: 0.379 Positive Predictive Value RNAalifold(20): 0.849 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.553 RNASLOpt: 0.467 Sensitivity RNAalifold(20): 0.407 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.756 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.596 Multilign(20): 0.521 Sensitivity RNAalifold(20): 0.443 Multilign(20): 0.428 Positive Predictive Value RNAalifold(20): 0.808 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	? RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.627 RNAwolf: 0.364 Sensitivity RNAalifold(20): 0.481 RNAwolf: 0.333 Positive Predictive Value RNAalifold(20): 0.823 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.595 Murlet(seed): 0.491 Sensitivity RNAalifold(20): 0.436 Murlet(seed): 0.269 Positive Predictive Value RNAalifold(20): 0.817 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.652 MCFold: 0.421 Sensitivity RNAalifold(20): 0.513 MCFold: 0.445 Positive Predictive Value RNAalifold(20): 0.833 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.644 Vsfold5: 0.406 Sensitivity RNAalifold(20): 0.491 Vsfold5: 0.347 Positive Predictive Value RNAalifold(20): 0.849 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.712 RDfolder: 0.529 Sensitivity RNAalifold(20): 0.555 RDfolder: 0.431 Positive Predictive Value RNAalifold(20): 0.918 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(seed): 0.249 Sensitivity RNAalifold(20): 0.491 RSpredict(seed): 0.110 Positive Predictive Value RNAalifold(20): 0.843 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 PPfold(seed): 0.026 Sensitivity RNAalifold(20): 0.481 PPfold(seed): 0.004 Positive Predictive Value RNAalifold(20): 0.823 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.565 NanoFolder: 0.316 Sensitivity RNAalifold(20): 0.432 NanoFolder: 0.324 Positive Predictive Value RNAalifold(20): 0.744 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.644 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.491 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.849 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-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	? Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.678 RNAalifold(20): 0.672 Sensitivity Multilign(seed): 0.543 RNAalifold(20): 0.536 Positive Predictive Value Multilign(seed): 0.852 RNAalifold(20): 0.851 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.557 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.620 RNAalifold(20): 0.619 Sensitivity TurboFold(20): 0.500 RNAalifold(20): 0.483 Positive Predictive Value TurboFold(20): 0.775 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.497 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 RNAalifold(20): 0.592 Sensitivity TurboFold(seed): 0.490 RNAalifold(20): 0.456 Positive Predictive Value TurboFold(seed): 0.729 RNAalifold(20): 0.774 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNAalifold(20): 0.619 Sensitivity PPfold(20): 0.514 RNAalifold(20): 0.483 Positive Predictive Value PPfold(20): 0.861 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 Carnac(seed): 0.197 Sensitivity RNAalifold(20): 0.477 Carnac(seed): 0.039 Positive Predictive Value RNAalifold(20): 0.828 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
RNASampler(20)	27 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RNASampler(20): 0.640 Sensitivity MXScarna(seed): 0.556 RNASampler(20): 0.489 Positive Predictive Value MXScarna(seed): 0.805 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.636 CentroidFold: 0.597 Sensitivity RNASampler(20): 0.484 CentroidFold: 0.506 Positive Predictive Value RNASampler(20): 0.840 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNASampler(20): 0.636 Sensitivity CentroidAlifold(20): 0.520 RNASampler(20): 0.484 Positive Predictive Value CentroidAlifold(20): 0.892 RNASampler(20): 0.840 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 RNASampler(20): 0.634 Sensitivity RNAalifold(20): 0.491 RNASampler(20): 0.477 Positive Predictive Value RNAalifold(20): 0.849 RNASampler(20): 0.844 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.634 Sfold: 0.590 Sensitivity RNASampler(20): 0.477 Sfold: 0.493 Positive Predictive Value RNASampler(20): 0.844 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.634 MXScarna(20): 0.628 Sensitivity RNASampler(20): 0.477 MXScarna(20): 0.523 Positive Predictive Value RNASampler(20): 0.844 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.97652614729e-06	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.634 Contrafold: 0.544 Sensitivity RNASampler(20): 0.477 Contrafold: 0.481 Positive Predictive Value RNASampler(20): 0.844 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.625 Fold: 0.610 Sensitivity RNASampler(20): 0.460 Fold: 0.542 Positive Predictive Value RNASampler(20): 0.851 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.634 HotKnots: 0.577 Sensitivity RNASampler(20): 0.477 HotKnots: 0.514 Positive Predictive Value RNASampler(20): 0.844 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.660 CentroidHomfold‑LAST: 0.654 Sensitivity RNASampler(20): 0.507 CentroidHomfold‑LAST: 0.524 Positive Predictive Value RNASampler(20): 0.865 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.637 IPknot: 0.571 Sensitivity RNASampler(20): 0.478 IPknot: 0.463 Positive Predictive Value RNASampler(20): 0.854 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.636 MaxExpect: 0.588 Sensitivity RNASampler(20): 0.484 MaxExpect: 0.516 Positive Predictive Value RNASampler(20): 0.840 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.634 UNAFold: 0.585 Sensitivity RNASampler(20): 0.477 UNAFold: 0.512 Positive Predictive Value RNASampler(20): 0.844 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.579 RNASampler(20): 0.569 Sensitivity ContextFold: 0.443 RNASampler(20): 0.419 Positive Predictive Value ContextFold: 0.763 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.634 RNAshapes: 0.577 Sensitivity RNASampler(20): 0.477 RNAshapes: 0.506 Positive Predictive Value RNASampler(20): 0.844 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.634 RNAfold: 0.567 Sensitivity RNASampler(20): 0.477 RNAfold: 0.503 Positive Predictive Value RNASampler(20): 0.844 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.634 PknotsRG: 0.579 Sensitivity RNASampler(20): 0.477 PknotsRG: 0.516 Positive Predictive Value RNASampler(20): 0.844 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	= RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.636 CentroidAlifold(seed): 0.629 Sensitivity RNASampler(20): 0.484 CentroidAlifold(seed): 0.430 Positive Predictive Value RNASampler(20): 0.840 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.00322321493779	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.625 ProbKnot: 0.586 Sensitivity RNASampler(20): 0.460 ProbKnot: 0.529 Positive Predictive Value RNASampler(20): 0.851 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Murlet(20): 0.582 Sensitivity RNASampler(20): 0.477 Murlet(20): 0.423 Positive Predictive Value RNASampler(20): 0.844 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Carnac(20): 0.582 Sensitivity RNASampler(20): 0.477 Carnac(20): 0.371 Positive Predictive Value RNASampler(20): 0.844 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.597 Afold: 0.518 Sensitivity RNASampler(20): 0.452 Afold: 0.469 Positive Predictive Value RNASampler(20): 0.792 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.634 RNAsubopt: 0.550 Sensitivity RNASampler(20): 0.477 RNAsubopt: 0.492 Positive Predictive Value RNASampler(20): 0.844 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.679 Cylofold: 0.608 Sensitivity RNASampler(20): 0.507 Cylofold: 0.523 Positive Predictive Value RNASampler(20): 0.912 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.634 McQFold: 0.524 Sensitivity RNASampler(20): 0.477 McQFold: 0.454 Positive Predictive Value RNASampler(20): 0.844 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.584 RNAalifold(seed): 0.572 Sensitivity RNASampler(20): 0.427 RNAalifold(seed): 0.356 Positive Predictive Value RNASampler(20): 0.803 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.655 Pknots: 0.530 Sensitivity RNASampler(20): 0.500 Pknots: 0.483 Positive Predictive Value RNASampler(20): 0.862 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ 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: 1.66062906821e-08	? RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RNASampler(20): 0.578 Sensitivity RNASampler(seed): 0.444 RNASampler(20): 0.477 Positive Predictive Value RNASampler(seed): 0.768 RNASampler(20): 0.704 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.640 RSpredict(20): 0.547 Sensitivity RNASampler(20): 0.489 RSpredict(20): 0.428 Positive Predictive Value RNASampler(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(20): 0.525 Sensitivity RNASampler(20): 0.477 Mastr(20): 0.346 Positive Predictive Value RNASampler(20): 0.844 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.634 Vsfold4: 0.450 Sensitivity RNASampler(20): 0.477 Vsfold4: 0.379 Positive Predictive Value RNASampler(20): 0.844 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.569 RNASLOpt: 0.467 Sensitivity RNASampler(20): 0.419 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.626 Multilign(20): 0.521 Sensitivity RNASampler(20): 0.455 Multilign(20): 0.428 Positive Predictive Value RNASampler(20): 0.868 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	? RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.637 RNAwolf: 0.364 Sensitivity RNASampler(20): 0.478 RNAwolf: 0.333 Positive Predictive Value RNASampler(20): 0.854 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 Murlet(seed): 0.491 Sensitivity RNASampler(20): 0.452 Murlet(seed): 0.269 Positive Predictive Value RNASampler(20): 0.825 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.667 MCFold: 0.421 Sensitivity RNASampler(20): 0.522 MCFold: 0.445 Positive Predictive Value RNASampler(20): 0.857 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.634 Vsfold5: 0.406 Sensitivity RNASampler(20): 0.477 Vsfold5: 0.347 Positive Predictive Value RNASampler(20): 0.844 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.744 RDfolder: 0.529 Sensitivity RNASampler(20): 0.587 RDfolder: 0.431 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RSpredict(seed): 0.249 Sensitivity RNASampler(20): 0.489 RSpredict(seed): 0.110 Positive Predictive Value RNASampler(20): 0.843 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 PPfold(seed): 0.026 Sensitivity RNASampler(20): 0.478 PPfold(seed): 0.004 Positive Predictive Value RNASampler(20): 0.854 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.567 NanoFolder: 0.316 Sensitivity RNASampler(20): 0.426 NanoFolder: 0.324 Positive Predictive Value RNASampler(20): 0.759 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.477 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.844 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 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	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.711 Multilign(seed): 0.678 Sensitivity RNASampler(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value RNASampler(20): 0.938 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(seed): 0.557 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.660 TurboFold(20): 0.620 Sensitivity RNASampler(20): 0.507 TurboFold(20): 0.500 Positive Predictive Value RNASampler(20): 0.865 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(20): 0.497 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.642 TurboFold(seed): 0.595 Sensitivity RNASampler(20): 0.487 TurboFold(seed): 0.490 Positive Predictive Value RNASampler(20): 0.853 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNASampler(20): 0.660 Sensitivity PPfold(20): 0.514 RNASampler(20): 0.507 Positive Predictive Value PPfold(20): 0.861 RNASampler(20): 0.865 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 Carnac(seed): 0.197 Sensitivity RNASampler(20): 0.481 Carnac(seed): 0.039 Positive Predictive Value RNASampler(20): 0.849 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08
Sfold	44 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.673 Sfold: 0.608 Sensitivity MXScarna(seed): 0.562 Sfold: 0.525 Positive Predictive Value MXScarna(seed): 0.809 Sfold: 0.708 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.577 Sfold: 0.548 Sensitivity CentroidFold: 0.493 Sfold: 0.470 Positive Predictive Value CentroidFold: 0.676 Sfold: 0.641 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Sfold: 0.589 Sensitivity CentroidAlifold(20): 0.520 Sfold: 0.495 Positive Predictive Value CentroidAlifold(20): 0.892 Sfold: 0.706 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.644 Sfold: 0.590 Sensitivity RNAalifold(20): 0.491 Sfold: 0.493 Positive Predictive Value RNAalifold(20): 0.849 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.634 Sfold: 0.590 Sensitivity RNASampler(20): 0.477 Sfold: 0.493 Positive Predictive Value RNASampler(20): 0.844 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08		- MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.628 Sfold: 0.590 Sensitivity MXScarna(20): 0.523 Sfold: 0.493 Positive Predictive Value MXScarna(20): 0.757 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	- Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.575 Sfold: 0.527 Sensitivity Contrafold: 0.511 Sfold: 0.448 Positive Predictive Value Contrafold: 0.648 Sfold: 0.621 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.681 Fold: 0.679 Sensitivity Sfold: 0.598 Fold: 0.618 Positive Predictive Value Sfold: 0.779 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.247700967591	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.669 HotKnots: 0.662 Sensitivity Sfold: 0.581 HotKnots: 0.600 Positive Predictive Value Sfold: 0.775 HotKnots: 0.736 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Sfold: 0.644 Sensitivity CentroidHomfold‑LAST: 0.515 Sfold: 0.549 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Sfold: 0.762 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 6.06606238843e-08	- IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.675 Sfold: 0.638 Sensitivity IPknot: 0.573 Sfold: 0.542 Positive Predictive Value IPknot: 0.801 Sfold: 0.758 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.617 Sfold: 0.595 Sensitivity MaxExpect: 0.540 Sfold: 0.501 Positive Predictive Value MaxExpect: 0.705 Sfold: 0.707 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.527 UNAFold: 0.508 Sensitivity Sfold: 0.448 UNAFold: 0.454 Positive Predictive Value Sfold: 0.621 UNAFold: 0.569 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.705 Sfold: 0.629 Sensitivity ContextFold: 0.594 Sfold: 0.536 Positive Predictive Value ContextFold: 0.843 Sfold: 0.744 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.669 RNAshapes: 0.650 Sensitivity Sfold: 0.581 RNAshapes: 0.580 Positive Predictive Value Sfold: 0.775 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.527 RNAfold: 0.504 Sensitivity Sfold: 0.448 RNAfold: 0.454 Positive Predictive Value Sfold: 0.621 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.527 PknotsRG: 0.495 Sensitivity Sfold: 0.448 PknotsRG: 0.447 Positive Predictive Value Sfold: 0.621 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs CentroidAlifold(seed) Matthews Correlation Coefficient Sfold: 0.605 CentroidAlifold(seed): 0.605 Sensitivity Sfold: 0.523 CentroidAlifold(seed): 0.419 Positive Predictive Value Sfold: 0.705 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.333157548069	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.667 ProbKnot: 0.646 Sensitivity Sfold: 0.583 ProbKnot: 0.597 Positive Predictive Value Sfold: 0.766 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.590 Murlet(20): 0.582 Sensitivity Sfold: 0.493 Murlet(20): 0.423 Positive Predictive Value Sfold: 0.709 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.13258597535e-06	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.590 Carnac(20): 0.582 Sensitivity Sfold: 0.493 Carnac(20): 0.371 Positive Predictive Value Sfold: 0.709 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.66995548893e-06	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.515 Afold: 0.491 Sensitivity Sfold: 0.438 Afold: 0.446 Positive Predictive Value Sfold: 0.604 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.669 RNAsubopt: 0.635 Sensitivity Sfold: 0.581 RNAsubopt: 0.574 Positive Predictive Value Sfold: 0.775 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.697 Cylofold: 0.648 Sensitivity Sfold: 0.603 Cylofold: 0.559 Positive Predictive Value Sfold: 0.810 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.526 McQFold: 0.443 Sensitivity Sfold: 0.446 McQFold: 0.348 Positive Predictive Value Sfold: 0.620 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.629 RNAalifold(seed): 0.593 Sensitivity Sfold: 0.544 RNAalifold(seed): 0.397 Positive Predictive Value Sfold: 0.730 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.691 Pknots: 0.634 Sensitivity Sfold: 0.598 Pknots: 0.575 Positive Predictive Value Sfold: 0.804 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-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 RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.721 RNASampler(seed): 0.673 Sensitivity Sfold: 0.637 RNASampler(seed): 0.535 Positive Predictive Value Sfold: 0.819 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.91441904741e-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: 3.85233844192e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.594 RSpredict(20): 0.547 Sensitivity Sfold: 0.500 RSpredict(20): 0.428 Positive Predictive Value Sfold: 0.710 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.590 Mastr(20): 0.525 Sensitivity Sfold: 0.493 Mastr(20): 0.346 Positive Predictive Value Sfold: 0.709 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.669 Vsfold4: 0.562 Sensitivity Sfold: 0.581 Vsfold4: 0.481 Positive Predictive Value Sfold: 0.775 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.629 RNASLOpt: 0.591 Sensitivity Sfold: 0.536 RNASLOpt: 0.498 Positive Predictive Value Sfold: 0.744 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.578 Multilign(20): 0.521 Sensitivity Sfold: 0.476 Multilign(20): 0.428 Positive Predictive Value Sfold: 0.709 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.21584974784e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.638 RNAwolf: 0.512 Sensitivity Sfold: 0.542 RNAwolf: 0.479 Positive Predictive Value Sfold: 0.758 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.682 Murlet(seed): 0.539 Sensitivity Sfold: 0.581 Murlet(seed): 0.337 Positive Predictive Value Sfold: 0.805 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.706 MCFold: 0.577 Sensitivity Sfold: 0.617 MCFold: 0.597 Positive Predictive Value Sfold: 0.813 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.668 Vsfold5: 0.528 Sensitivity Sfold: 0.580 Vsfold5: 0.458 Positive Predictive Value Sfold: 0.774 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.717 RDfolder: 0.596 Sensitivity Sfold: 0.624 RDfolder: 0.495 Positive Predictive Value Sfold: 0.833 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.608 RSpredict(seed): 0.314 Sensitivity Sfold: 0.525 RSpredict(seed): 0.161 Positive Predictive Value Sfold: 0.708 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.539 PPfold(seed): 0.102 Sensitivity Sfold: 0.426 PPfold(seed): 0.020 Positive Predictive Value Sfold: 0.691 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.45186852942e-09	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.614 NanoFolder: 0.490 Sensitivity Sfold: 0.520 NanoFolder: 0.495 Positive Predictive Value Sfold: 0.733 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.605 Mastr(seed): 0.258 Sensitivity Sfold: 0.520 Mastr(seed): 0.075 Positive Predictive Value Sfold: 0.707 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.655 Multilign(seed): 0.593 Sensitivity Sfold: 0.532 Multilign(seed): 0.475 Positive Predictive Value Sfold: 0.816 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Sfold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 Sfold: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.620 Sfold: 0.610 Sensitivity TurboFold(20): 0.500 Sfold: 0.500 Positive Predictive Value TurboFold(20): 0.775 Sfold: 0.751 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Sfold: 0.507 Sensitivity PETfold_pre2.0(20): 0.497 Sfold: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.590 TurboFold(seed): 0.550 Sensitivity Sfold: 0.481 TurboFold(seed): 0.456 Positive Predictive Value Sfold: 0.731 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.663 Sfold: 0.610 Sensitivity PPfold(20): 0.514 Sfold: 0.500 Positive Predictive Value PPfold(20): 0.861 Sfold: 0.751 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.684 Carnac(seed): 0.260 Sensitivity Sfold: 0.590 Carnac(seed): 0.068 Positive Predictive Value Sfold: 0.797 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	27 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 MXScarna(20): 0.634 Sensitivity MXScarna(seed): 0.556 MXScarna(20): 0.530 Positive Predictive Value MXScarna(seed): 0.805 MXScarna(20): 0.761 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.630 CentroidFold: 0.597 Sensitivity MXScarna(20): 0.526 CentroidFold: 0.506 Positive Predictive Value MXScarna(20): 0.758 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MXScarna(20): 0.630 Sensitivity CentroidAlifold(20): 0.520 MXScarna(20): 0.526 Positive Predictive Value CentroidAlifold(20): 0.892 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 MXScarna(20): 0.628 Sensitivity RNAalifold(20): 0.491 MXScarna(20): 0.523 Positive Predictive Value RNAalifold(20): 0.849 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.634 MXScarna(20): 0.628 Sensitivity RNASampler(20): 0.477 MXScarna(20): 0.523 Positive Predictive Value RNASampler(20): 0.844 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.97652614729e-06	28 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.628 Sfold: 0.590 Sensitivity MXScarna(20): 0.523 Sfold: 0.493 Positive Predictive Value MXScarna(20): 0.757 Sfold: 0.709 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08		+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.628 Contrafold: 0.544 Sensitivity MXScarna(20): 0.523 Contrafold: 0.481 Positive Predictive Value MXScarna(20): 0.757 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.628 Fold: 0.610 Sensitivity MXScarna(20): 0.520 Fold: 0.542 Positive Predictive Value MXScarna(20): 0.762 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.628 HotKnots: 0.577 Sensitivity MXScarna(20): 0.523 HotKnots: 0.514 Positive Predictive Value MXScarna(20): 0.757 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 MXScarna(20): 0.598 Sensitivity CentroidHomfold‑LAST: 0.524 MXScarna(20): 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.822 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.586 IPknot: 0.571 Sensitivity MXScarna(20): 0.474 IPknot: 0.463 Positive Predictive Value MXScarna(20): 0.731 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.630 MaxExpect: 0.588 Sensitivity MXScarna(20): 0.526 MaxExpect: 0.516 Positive Predictive Value MXScarna(20): 0.758 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.628 UNAFold: 0.585 Sensitivity MXScarna(20): 0.523 UNAFold: 0.512 Positive Predictive Value MXScarna(20): 0.757 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.579 MXScarna(20): 0.501 Sensitivity ContextFold: 0.443 MXScarna(20): 0.401 Positive Predictive Value ContextFold: 0.763 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.628 RNAshapes: 0.577 Sensitivity MXScarna(20): 0.523 RNAshapes: 0.506 Positive Predictive Value MXScarna(20): 0.757 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.628 RNAfold: 0.567 Sensitivity MXScarna(20): 0.523 RNAfold: 0.503 Positive Predictive Value MXScarna(20): 0.757 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.628 PknotsRG: 0.579 Sensitivity MXScarna(20): 0.523 PknotsRG: 0.516 Positive Predictive Value MXScarna(20): 0.757 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.630 CentroidAlifold(seed): 0.629 Sensitivity MXScarna(20): 0.526 CentroidAlifold(seed): 0.430 Positive Predictive Value MXScarna(20): 0.758 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0920574641616	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.628 ProbKnot: 0.586 Sensitivity MXScarna(20): 0.520 ProbKnot: 0.529 Positive Predictive Value MXScarna(20): 0.762 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Murlet(20): 0.582 Sensitivity MXScarna(20): 0.523 Murlet(20): 0.423 Positive Predictive Value MXScarna(20): 0.757 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Carnac(20): 0.582 Sensitivity MXScarna(20): 0.523 Carnac(20): 0.371 Positive Predictive Value MXScarna(20): 0.757 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.602 Afold: 0.518 Sensitivity MXScarna(20): 0.506 Afold: 0.469 Positive Predictive Value MXScarna(20): 0.719 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.628 RNAsubopt: 0.550 Sensitivity MXScarna(20): 0.523 RNAsubopt: 0.492 Positive Predictive Value MXScarna(20): 0.757 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.682 Cylofold: 0.608 Sensitivity MXScarna(20): 0.564 Cylofold: 0.523 Positive Predictive Value MXScarna(20): 0.829 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.628 McQFold: 0.524 Sensitivity MXScarna(20): 0.523 McQFold: 0.454 Positive Predictive Value MXScarna(20): 0.757 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.603 RNAalifold(seed): 0.572 Sensitivity MXScarna(20): 0.488 RNAalifold(seed): 0.356 Positive Predictive Value MXScarna(20): 0.749 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.644 Pknots: 0.530 Sensitivity MXScarna(20): 0.540 Pknots: 0.483 Positive Predictive Value MXScarna(20): 0.773 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ 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: 2.64318034126e-08	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 MXScarna(20): 0.557 Sensitivity RNASampler(seed): 0.444 MXScarna(20): 0.469 Positive Predictive Value RNASampler(seed): 0.768 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.634 RSpredict(20): 0.547 Sensitivity MXScarna(20): 0.530 RSpredict(20): 0.428 Positive Predictive Value MXScarna(20): 0.761 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Mastr(20): 0.525 Sensitivity MXScarna(20): 0.523 Mastr(20): 0.346 Positive Predictive Value MXScarna(20): 0.757 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.628 Vsfold4: 0.450 Sensitivity MXScarna(20): 0.523 Vsfold4: 0.379 Positive Predictive Value MXScarna(20): 0.757 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.501 RNASLOpt: 0.467 Sensitivity MXScarna(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.632 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Multilign(20): 0.521 Sensitivity MXScarna(20): 0.518 Multilign(20): 0.428 Positive Predictive Value MXScarna(20): 0.761 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.9460272886e-09	? MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.586 RNAwolf: 0.364 Sensitivity MXScarna(20): 0.474 RNAwolf: 0.333 Positive Predictive Value MXScarna(20): 0.731 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.625 Murlet(seed): 0.491 Sensitivity MXScarna(20): 0.506 Murlet(seed): 0.269 Positive Predictive Value MXScarna(20): 0.775 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.651 MCFold: 0.421 Sensitivity MXScarna(20): 0.546 MCFold: 0.445 Positive Predictive Value MXScarna(20): 0.779 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.628 Vsfold5: 0.406 Sensitivity MXScarna(20): 0.523 Vsfold5: 0.347 Positive Predictive Value MXScarna(20): 0.757 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.695 RDfolder: 0.529 Sensitivity MXScarna(20): 0.564 RDfolder: 0.431 Positive Predictive Value MXScarna(20): 0.862 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.634 RSpredict(seed): 0.249 Sensitivity MXScarna(20): 0.530 RSpredict(seed): 0.110 Positive Predictive Value MXScarna(20): 0.761 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.586 PPfold(seed): 0.026 Sensitivity MXScarna(20): 0.474 PPfold(seed): 0.004 Positive Predictive Value MXScarna(20): 0.731 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.524 NanoFolder: 0.316 Sensitivity MXScarna(20): 0.439 NanoFolder: 0.324 Positive Predictive Value MXScarna(20): 0.631 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.628 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.523 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.757 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-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	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.678 MXScarna(20): 0.664 Sensitivity Multilign(seed): 0.543 MXScarna(20): 0.565 Positive Predictive Value Multilign(seed): 0.852 MXScarna(20): 0.788 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(seed): 0.557 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.620 MXScarna(20): 0.598 Sensitivity TurboFold(20): 0.500 MXScarna(20): 0.490 Positive Predictive Value TurboFold(20): 0.775 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 MXScarna(20): 0.569 Sensitivity TurboFold(seed): 0.490 MXScarna(20): 0.464 Positive Predictive Value TurboFold(seed): 0.729 MXScarna(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(20): 0.598 Sensitivity PPfold(20): 0.514 MXScarna(20): 0.490 Positive Predictive Value PPfold(20): 0.861 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.632 Carnac(seed): 0.197 Sensitivity MXScarna(20): 0.528 Carnac(seed): 0.039 Positive Predictive Value MXScarna(20): 0.761 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
Contrafold	44 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.673 Contrafold: 0.599 Sensitivity MXScarna(seed): 0.562 Contrafold: 0.544 Positive Predictive Value MXScarna(seed): 0.809 Contrafold: 0.664 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.577 Contrafold: 0.574 Sensitivity CentroidFold: 0.493 Contrafold: 0.516 Positive Predictive Value CentroidFold: 0.676 Contrafold: 0.639 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 9.17559933998e-05	26 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Contrafold: 0.552 Sensitivity CentroidAlifold(20): 0.520 Contrafold: 0.490 Positive Predictive Value CentroidAlifold(20): 0.892 Contrafold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.644 Contrafold: 0.544 Sensitivity RNAalifold(20): 0.491 Contrafold: 0.481 Positive Predictive Value RNAalifold(20): 0.849 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.634 Contrafold: 0.544 Sensitivity RNASampler(20): 0.477 Contrafold: 0.481 Positive Predictive Value RNASampler(20): 0.844 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	121 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.575 Sfold: 0.527 Sensitivity Contrafold: 0.511 Sfold: 0.448 Positive Predictive Value Contrafold: 0.648 Sfold: 0.621 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.628 Contrafold: 0.544 Sensitivity MXScarna(20): 0.523 Contrafold: 0.481 Positive Predictive Value MXScarna(20): 0.757 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08		= Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.679 Fold: 0.679 Sensitivity Contrafold: 0.616 Fold: 0.618 Positive Predictive Value Contrafold: 0.753 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.0452037747897	= HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.662 Contrafold: 0.660 Sensitivity HotKnots: 0.600 Contrafold: 0.592 Positive Predictive Value HotKnots: 0.736 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.00636070127375	- CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Contrafold: 0.662 Sensitivity CentroidHomfold‑LAST: 0.515 Contrafold: 0.579 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Contrafold: 0.764 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 9.17559933998e-05	- IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.675 Contrafold: 0.658 Sensitivity IPknot: 0.573 Contrafold: 0.576 Positive Predictive Value IPknot: 0.801 Contrafold: 0.759 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.626 MaxExpect: 0.617 Sensitivity Contrafold: 0.551 MaxExpect: 0.540 Positive Predictive Value Contrafold: 0.712 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.575 UNAFold: 0.508 Sensitivity Contrafold: 0.511 UNAFold: 0.454 Positive Predictive Value Contrafold: 0.648 UNAFold: 0.569 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.705 Contrafold: 0.649 Sensitivity ContextFold: 0.594 Contrafold: 0.568 Positive Predictive Value ContextFold: 0.843 Contrafold: 0.749 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.660 RNAshapes: 0.650 Sensitivity Contrafold: 0.592 RNAshapes: 0.580 Positive Predictive Value Contrafold: 0.740 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.575 RNAfold: 0.504 Sensitivity Contrafold: 0.511 RNAfold: 0.454 Positive Predictive Value Contrafold: 0.648 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.575 PknotsRG: 0.495 Sensitivity Contrafold: 0.511 PknotsRG: 0.447 Positive Predictive Value Contrafold: 0.648 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Contrafold: 0.596 Sensitivity CentroidAlifold(seed): 0.419 Contrafold: 0.541 Positive Predictive Value CentroidAlifold(seed): 0.878 Contrafold: 0.661 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.00517730549486	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.659 ProbKnot: 0.646 Sensitivity Contrafold: 0.597 ProbKnot: 0.597 Positive Predictive Value Contrafold: 0.732 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.582 Contrafold: 0.544 Sensitivity Murlet(20): 0.423 Contrafold: 0.481 Positive Predictive Value Murlet(20): 0.804 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.582 Contrafold: 0.544 Sensitivity Carnac(20): 0.371 Contrafold: 0.481 Positive Predictive Value Carnac(20): 0.915 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.567 Afold: 0.491 Sensitivity Contrafold: 0.505 Afold: 0.446 Positive Predictive Value Contrafold: 0.637 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.660 RNAsubopt: 0.635 Sensitivity Contrafold: 0.592 RNAsubopt: 0.574 Positive Predictive Value Contrafold: 0.740 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.696 Cylofold: 0.648 Sensitivity Contrafold: 0.622 Cylofold: 0.559 Positive Predictive Value Contrafold: 0.785 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.574 McQFold: 0.443 Sensitivity Contrafold: 0.510 McQFold: 0.348 Positive Predictive Value Contrafold: 0.647 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.608 RNAalifold(seed): 0.593 Sensitivity Contrafold: 0.552 RNAalifold(seed): 0.397 Positive Predictive Value Contrafold: 0.673 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.681 Pknots: 0.634 Sensitivity Contrafold: 0.607 Pknots: 0.575 Positive Predictive Value Contrafold: 0.770 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-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 RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.689 RNASampler(seed): 0.673 Sensitivity Contrafold: 0.630 RNASampler(seed): 0.535 Positive Predictive Value Contrafold: 0.759 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.44851456278e-08	+ 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 RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.556 RSpredict(20): 0.547 Sensitivity Contrafold: 0.495 RSpredict(20): 0.428 Positive Predictive Value Contrafold: 0.630 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.69838533668e-06	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.544 Mastr(20): 0.525 Sensitivity Contrafold: 0.481 Mastr(20): 0.346 Positive Predictive Value Contrafold: 0.619 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.72695708134e-06	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.660 Vsfold4: 0.562 Sensitivity Contrafold: 0.592 Vsfold4: 0.481 Positive Predictive Value Contrafold: 0.740 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.649 RNASLOpt: 0.591 Sensitivity Contrafold: 0.568 RNASLOpt: 0.498 Positive Predictive Value Contrafold: 0.749 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.528 Multilign(20): 0.521 Sensitivity Contrafold: 0.458 Multilign(20): 0.428 Positive Predictive Value Contrafold: 0.615 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000723083277971	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.658 RNAwolf: 0.512 Sensitivity Contrafold: 0.576 RNAwolf: 0.479 Positive Predictive Value Contrafold: 0.759 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.654 Murlet(seed): 0.539 Sensitivity Contrafold: 0.582 Murlet(seed): 0.337 Positive Predictive Value Contrafold: 0.740 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.689 MCFold: 0.577 Sensitivity Contrafold: 0.618 MCFold: 0.597 Positive Predictive Value Contrafold: 0.773 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.659 Vsfold5: 0.528 Sensitivity Contrafold: 0.591 Vsfold5: 0.458 Positive Predictive Value Contrafold: 0.739 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.726 RDfolder: 0.596 Sensitivity Contrafold: 0.644 RDfolder: 0.495 Positive Predictive Value Contrafold: 0.825 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.599 RSpredict(seed): 0.314 Sensitivity Contrafold: 0.544 RSpredict(seed): 0.161 Positive Predictive Value Contrafold: 0.664 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.559 PPfold(seed): 0.102 Sensitivity Contrafold: 0.471 PPfold(seed): 0.020 Positive Predictive Value Contrafold: 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.656 NanoFolder: 0.490 Sensitivity Contrafold: 0.574 NanoFolder: 0.495 Positive Predictive Value Contrafold: 0.756 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.589 Mastr(seed): 0.258 Sensitivity Contrafold: 0.533 Mastr(seed): 0.075 Positive Predictive Value Contrafold: 0.655 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.606 Multilign(seed): 0.593 Sensitivity Contrafold: 0.506 Multilign(seed): 0.475 Positive Predictive Value Contrafold: 0.734 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.551 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Contrafold: 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.620 Contrafold: 0.589 Sensitivity TurboFold(20): 0.500 Contrafold: 0.507 Positive Predictive Value TurboFold(20): 0.775 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Contrafold: 0.511 Sensitivity PETfold_pre2.0(20): 0.497 Contrafold: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.790 Contrafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.573 TurboFold(seed): 0.550 Sensitivity Contrafold: 0.488 TurboFold(seed): 0.456 Positive Predictive Value Contrafold: 0.680 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.663 Contrafold: 0.589 Sensitivity PPfold(20): 0.514 Contrafold: 0.507 Positive Predictive Value PPfold(20): 0.861 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.649 Carnac(seed): 0.260 Sensitivity Contrafold: 0.583 Carnac(seed): 0.068 Positive Predictive Value Contrafold: 0.728 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	31 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.665 Fold: 0.625 Sensitivity MXScarna(seed): 0.555 Fold: 0.569 Positive Predictive Value MXScarna(seed): 0.801 Fold: 0.690 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.693 Fold: 0.679 Sensitivity CentroidFold: 0.608 Fold: 0.618 Positive Predictive Value CentroidFold: 0.793 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.671 Fold: 0.610 Sensitivity CentroidAlifold(20): 0.500 Fold: 0.542 Positive Predictive Value CentroidAlifold(20): 0.904 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.45076534967e-08	18 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.626 Fold: 0.610 Sensitivity RNAalifold(20): 0.468 Fold: 0.542 Positive Predictive Value RNAalifold(20): 0.841 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	18 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.625 Fold: 0.610 Sensitivity RNASampler(20): 0.460 Fold: 0.542 Positive Predictive Value RNASampler(20): 0.851 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	82 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.681 Fold: 0.679 Sensitivity Sfold: 0.598 Fold: 0.618 Positive Predictive Value Sfold: 0.779 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.247700967591	18 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.628 Fold: 0.610 Sensitivity MXScarna(20): 0.520 Fold: 0.542 Positive Predictive Value MXScarna(20): 0.762 Fold: 0.689 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	82 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.679 Fold: 0.679 Sensitivity Contrafold: 0.616 Fold: 0.618 Positive Predictive Value Contrafold: 0.753 Fold: 0.751 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.0452037747897		= Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.679 HotKnots: 0.677 Sensitivity Fold: 0.618 HotKnots: 0.621 Positive Predictive Value Fold: 0.751 HotKnots: 0.742 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.00238364898467	- CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Fold: 0.611 Sensitivity CentroidHomfold‑LAST: 0.515 Fold: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Fold: 0.692 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	- IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.675 Fold: 0.611 Sensitivity IPknot: 0.573 Fold: 0.545 Positive Predictive Value IPknot: 0.801 Fold: 0.692 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.679 MaxExpect: 0.665 Sensitivity Fold: 0.618 MaxExpect: 0.601 Positive Predictive Value Fold: 0.751 MaxExpect: 0.740 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.679 UNAFold: 0.670 Sensitivity Fold: 0.618 UNAFold: 0.608 Positive Predictive Value Fold: 0.751 UNAFold: 0.743 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 2.82781450476e-07	- ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.705 Fold: 0.609 Sensitivity ContextFold: 0.594 Fold: 0.543 Positive Predictive Value ContextFold: 0.843 Fold: 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.679 RNAshapes: 0.671 Sensitivity Fold: 0.618 RNAshapes: 0.606 Positive Predictive Value Fold: 0.751 RNAshapes: 0.746 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.679 RNAfold: 0.662 Sensitivity Fold: 0.618 RNAfold: 0.604 Positive Predictive Value Fold: 0.751 RNAfold: 0.729 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.679 PknotsRG: 0.659 Sensitivity Fold: 0.618 PknotsRG: 0.604 Positive Predictive Value Fold: 0.751 PknotsRG: 0.722 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Fold vs CentroidAlifold(seed) Matthews Correlation Coefficient Fold: 0.625 CentroidAlifold(seed): 0.609 Sensitivity Fold: 0.569 CentroidAlifold(seed): 0.424 Positive Predictive Value Fold: 0.690 CentroidAlifold(seed): 0.877 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.76761760679e-06	+ Fold vs ProbKnot Matthews Correlation Coefficient Fold: 0.660 ProbKnot: 0.646 Sensitivity Fold: 0.600 ProbKnot: 0.597 Positive Predictive Value Fold: 0.730 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.610 Murlet(20): 0.575 Sensitivity Fold: 0.542 Murlet(20): 0.413 Positive Predictive Value Fold: 0.689 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.82974185391e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.610 Carnac(20): 0.558 Sensitivity Fold: 0.542 Carnac(20): 0.339 Positive Predictive Value Fold: 0.689 Carnac(20): 0.924 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.693 Afold: 0.672 Sensitivity Fold: 0.643 Afold: 0.629 Positive Predictive Value Fold: 0.751 Afold: 0.722 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.679 RNAsubopt: 0.663 Sensitivity Fold: 0.618 RNAsubopt: 0.605 Positive Predictive Value Fold: 0.751 RNAsubopt: 0.732 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.701 Cylofold: 0.648 Sensitivity Fold: 0.629 Cylofold: 0.559 Positive Predictive Value Fold: 0.786 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.677 McQFold: 0.646 Sensitivity Fold: 0.616 McQFold: 0.568 Positive Predictive Value Fold: 0.749 McQFold: 0.740 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.588 RNAalifold(seed): 0.571 Sensitivity Fold: 0.543 RNAalifold(seed): 0.375 Positive Predictive Value Fold: 0.640 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 7.71892784613e-07	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.714 Pknots: 0.660 Sensitivity Fold: 0.645 Pknots: 0.599 Positive Predictive Value Fold: 0.796 Pknots: 0.734 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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	- RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.662 Fold: 0.642 Sensitivity RNASampler(seed): 0.525 Fold: 0.607 Positive Predictive Value RNASampler(seed): 0.839 Fold: 0.684 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.78614631659e-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: 8.68922211961e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.610 RSpredict(20): 0.524 Sensitivity Fold: 0.542 RSpredict(20): 0.403 Positive Predictive Value Fold: 0.689 RSpredict(20): 0.684 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.610 Mastr(20): 0.491 Sensitivity Fold: 0.542 Mastr(20): 0.300 Positive Predictive Value Fold: 0.689 Mastr(20): 0.808 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.679 Vsfold4: 0.571 Sensitivity Fold: 0.618 Vsfold4: 0.494 Positive Predictive Value Fold: 0.751 Vsfold4: 0.666 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.609 RNASLOpt: 0.591 Sensitivity Fold: 0.543 RNASLOpt: 0.498 Positive Predictive Value Fold: 0.690 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.596 Multilign(20): 0.521 Sensitivity Fold: 0.524 Multilign(20): 0.428 Positive Predictive Value Fold: 0.685 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.95402773876e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.611 RNAwolf: 0.512 Sensitivity Fold: 0.545 RNAwolf: 0.479 Positive Predictive Value Fold: 0.692 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.648 Murlet(seed): 0.542 Sensitivity Fold: 0.588 Murlet(seed): 0.339 Positive Predictive Value Fold: 0.719 Murlet(seed): 0.871 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.715 MCFold: 0.607 Sensitivity Fold: 0.651 MCFold: 0.627 Positive Predictive Value Fold: 0.791 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.678 Vsfold5: 0.538 Sensitivity Fold: 0.616 Vsfold5: 0.470 Positive Predictive Value Fold: 0.750 Vsfold5: 0.621 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.731 RDfolder: 0.622 Sensitivity Fold: 0.663 RDfolder: 0.524 Positive Predictive Value Fold: 0.812 RDfolder: 0.746 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.625 RSpredict(seed): 0.288 Sensitivity Fold: 0.569 RSpredict(seed): 0.145 Positive Predictive Value Fold: 0.690 RSpredict(seed): 0.578 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.516 PPfold(seed): 0.102 Sensitivity Fold: 0.443 PPfold(seed): 0.020 Positive Predictive Value Fold: 0.610 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.629 NanoFolder: 0.490 Sensitivity Fold: 0.559 NanoFolder: 0.495 Positive Predictive Value Fold: 0.714 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.625 Mastr(seed): 0.279 Sensitivity Fold: 0.569 Mastr(seed): 0.088 Positive Predictive Value Fold: 0.690 Mastr(seed): 0.886 Number of pairs reference - predicted secondary structure: 31 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	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.593 Fold: 0.572 Sensitivity Multilign(seed): 0.475 Fold: 0.481 Positive Predictive Value Multilign(seed): 0.750 Fold: 0.691 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Fold: 0.465 Sensitivity PETfold_pre2.0(seed): 0.551 Fold: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Fold: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.620 Fold: 0.546 Sensitivity TurboFold(20): 0.500 Fold: 0.476 Positive Predictive Value TurboFold(20): 0.775 Fold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Fold: 0.429 Sensitivity PETfold_pre2.0(20): 0.497 Fold: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.790 Fold: 0.496 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.550 Fold: 0.497 Sensitivity TurboFold(seed): 0.456 Fold: 0.431 Positive Predictive Value TurboFold(seed): 0.672 Fold: 0.581 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.663 Fold: 0.546 Sensitivity PPfold(20): 0.514 Fold: 0.476 Positive Predictive Value PPfold(20): 0.861 Fold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.657 Carnac(seed): 0.275 Sensitivity Fold: 0.594 Carnac(seed): 0.076 Positive Predictive Value Fold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08
HotKnots	44 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.673 HotKnots: 0.601 Sensitivity MXScarna(seed): 0.562 HotKnots: 0.549 Positive Predictive Value MXScarna(seed): 0.809 HotKnots: 0.663 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.676 HotKnots: 0.662 Sensitivity CentroidFold: 0.591 HotKnots: 0.603 Positive Predictive Value CentroidFold: 0.777 HotKnots: 0.731 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.680 HotKnots: 0.577 Sensitivity CentroidAlifold(20): 0.520 HotKnots: 0.517 Positive Predictive Value CentroidAlifold(20): 0.892 HotKnots: 0.648 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.644 HotKnots: 0.577 Sensitivity RNAalifold(20): 0.491 HotKnots: 0.514 Positive Predictive Value RNAalifold(20): 0.849 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.634 HotKnots: 0.577 Sensitivity RNASampler(20): 0.477 HotKnots: 0.514 Positive Predictive Value RNASampler(20): 0.844 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.669 HotKnots: 0.662 Sensitivity Sfold: 0.581 HotKnots: 0.600 Positive Predictive Value Sfold: 0.775 HotKnots: 0.736 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.628 HotKnots: 0.577 Sensitivity MXScarna(20): 0.523 HotKnots: 0.514 Positive Predictive Value MXScarna(20): 0.757 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.662 Contrafold: 0.660 Sensitivity HotKnots: 0.600 Contrafold: 0.592 Positive Predictive Value HotKnots: 0.736 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.00636070127375	82 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.679 HotKnots: 0.677 Sensitivity Fold: 0.618 HotKnots: 0.621 Positive Predictive Value Fold: 0.751 HotKnots: 0.742 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.00238364898467		- CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 HotKnots: 0.646 Sensitivity CentroidHomfold‑LAST: 0.515 HotKnots: 0.581 Positive Predictive Value CentroidHomfold‑LAST: 0.873 HotKnots: 0.726 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 4.1569883686e-08	- IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.675 HotKnots: 0.641 Sensitivity IPknot: 0.573 HotKnots: 0.577 Positive Predictive Value IPknot: 0.801 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.661 MaxExpect: 0.653 Sensitivity HotKnots: 0.602 MaxExpect: 0.587 Positive Predictive Value HotKnots: 0.729 MaxExpect: 0.731 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	- UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.664 HotKnots: 0.662 Sensitivity UNAFold: 0.595 HotKnots: 0.600 Positive Predictive Value UNAFold: 0.747 HotKnots: 0.736 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.64686539471e-05	- ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.705 HotKnots: 0.638 Sensitivity ContextFold: 0.594 HotKnots: 0.579 Positive Predictive Value ContextFold: 0.843 HotKnots: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.662 RNAshapes: 0.650 Sensitivity HotKnots: 0.600 RNAshapes: 0.580 Positive Predictive Value HotKnots: 0.736 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.662 RNAfold: 0.651 Sensitivity HotKnots: 0.600 RNAfold: 0.587 Positive Predictive Value HotKnots: 0.736 RNAfold: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.662 PknotsRG: 0.646 Sensitivity HotKnots: 0.600 PknotsRG: 0.585 Positive Predictive Value HotKnots: 0.736 PknotsRG: 0.718 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 HotKnots: 0.599 Sensitivity CentroidAlifold(seed): 0.419 HotKnots: 0.547 Positive Predictive Value CentroidAlifold(seed): 0.878 HotKnots: 0.660 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.000451186043411	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.659 ProbKnot: 0.646 Sensitivity HotKnots: 0.604 ProbKnot: 0.597 Positive Predictive Value HotKnots: 0.722 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.582 HotKnots: 0.577 Sensitivity Murlet(20): 0.423 HotKnots: 0.514 Positive Predictive Value Murlet(20): 0.804 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0546456716999	- Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.582 HotKnots: 0.577 Sensitivity Carnac(20): 0.371 HotKnots: 0.514 Positive Predictive Value Carnac(20): 0.915 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.95331270335e-05	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.670 Afold: 0.647 Sensitivity HotKnots: 0.614 Afold: 0.595 Positive Predictive Value HotKnots: 0.735 Afold: 0.709 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.662 RNAsubopt: 0.635 Sensitivity HotKnots: 0.600 RNAsubopt: 0.574 Positive Predictive Value HotKnots: 0.736 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.696 Cylofold: 0.648 Sensitivity HotKnots: 0.629 Cylofold: 0.559 Positive Predictive Value HotKnots: 0.775 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.661 McQFold: 0.620 Sensitivity HotKnots: 0.598 McQFold: 0.540 Positive Predictive Value HotKnots: 0.735 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.620 RNAalifold(seed): 0.593 Sensitivity HotKnots: 0.571 RNAalifold(seed): 0.397 Positive Predictive Value HotKnots: 0.677 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.686 Pknots: 0.634 Sensitivity HotKnots: 0.616 Pknots: 0.575 Positive Predictive Value HotKnots: 0.770 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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 RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.699 RNASampler(seed): 0.673 Sensitivity HotKnots: 0.653 RNASampler(seed): 0.535 Positive Predictive Value HotKnots: 0.753 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.52299983238e-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: 4.48494289621e-08	+ HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.581 RSpredict(20): 0.547 Sensitivity HotKnots: 0.521 RSpredict(20): 0.428 Positive Predictive Value HotKnots: 0.653 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.577 Mastr(20): 0.525 Sensitivity HotKnots: 0.514 Mastr(20): 0.346 Positive Predictive Value HotKnots: 0.652 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.662 Vsfold4: 0.562 Sensitivity HotKnots: 0.600 Vsfold4: 0.481 Positive Predictive Value HotKnots: 0.736 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.638 RNASLOpt: 0.591 Sensitivity HotKnots: 0.579 RNASLOpt: 0.498 Positive Predictive Value HotKnots: 0.709 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.599 Multilign(20): 0.521 Sensitivity HotKnots: 0.524 Multilign(20): 0.428 Positive Predictive Value HotKnots: 0.690 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.78774507289e-09	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.641 RNAwolf: 0.512 Sensitivity HotKnots: 0.577 RNAwolf: 0.479 Positive Predictive Value HotKnots: 0.719 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.677 Murlet(seed): 0.539 Sensitivity HotKnots: 0.608 Murlet(seed): 0.337 Positive Predictive Value HotKnots: 0.759 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.698 MCFold: 0.577 Sensitivity HotKnots: 0.633 MCFold: 0.597 Positive Predictive Value HotKnots: 0.776 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.662 Vsfold5: 0.528 Sensitivity HotKnots: 0.599 Vsfold5: 0.458 Positive Predictive Value HotKnots: 0.736 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.723 RDfolder: 0.596 Sensitivity HotKnots: 0.650 RDfolder: 0.495 Positive Predictive Value HotKnots: 0.813 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.601 RSpredict(seed): 0.314 Sensitivity HotKnots: 0.549 RSpredict(seed): 0.161 Positive Predictive Value HotKnots: 0.663 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.566 PPfold(seed): 0.102 Sensitivity HotKnots: 0.487 PPfold(seed): 0.020 Positive Predictive Value HotKnots: 0.664 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.630 NanoFolder: 0.490 Sensitivity HotKnots: 0.567 NanoFolder: 0.495 Positive Predictive Value HotKnots: 0.708 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.598 Mastr(seed): 0.258 Sensitivity HotKnots: 0.543 Mastr(seed): 0.075 Positive Predictive Value HotKnots: 0.662 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.672 Multilign(seed): 0.593 Sensitivity HotKnots: 0.563 Multilign(seed): 0.475 Positive Predictive Value HotKnots: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 HotKnots: 0.518 Sensitivity PETfold_pre2.0(seed): 0.551 HotKnots: 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 HotKnots: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.636 TurboFold(20): 0.620 Sensitivity HotKnots: 0.555 TurboFold(20): 0.500 Positive Predictive Value HotKnots: 0.735 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 HotKnots: 0.561 Sensitivity PETfold_pre2.0(20): 0.497 HotKnots: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 HotKnots: 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.628 TurboFold(seed): 0.550 Sensitivity HotKnots: 0.551 TurboFold(seed): 0.456 Positive Predictive Value HotKnots: 0.722 TurboFold(seed): 0.672 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): 0.663 HotKnots: 0.636 Sensitivity PPfold(20): 0.514 HotKnots: 0.555 Positive Predictive Value PPfold(20): 0.861 HotKnots: 0.735 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.678 Carnac(seed): 0.260 Sensitivity HotKnots: 0.612 Carnac(seed): 0.068 Positive Predictive Value HotKnots: 0.757 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	12 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 MXScarna(seed): 0.621 Sensitivity CentroidHomfold‑LAST: 0.501 MXScarna(seed): 0.496 Positive Predictive Value CentroidHomfold‑LAST: 0.808 MXScarna(seed): 0.782 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.54564345795e-08	44 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 CentroidFold: 0.667 Sensitivity CentroidHomfold‑LAST: 0.515 CentroidFold: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.873 CentroidFold: 0.792 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 0.716668360784	9 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.684 CentroidHomfold‑LAST: 0.654 Sensitivity CentroidAlifold(20): 0.517 CentroidHomfold‑LAST: 0.524 Positive Predictive Value CentroidAlifold(20): 0.909 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RNAalifold(20): 0.619 Sensitivity CentroidHomfold‑LAST: 0.524 RNAalifold(20): 0.483 Positive Predictive Value CentroidHomfold‑LAST: 0.822 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.660 CentroidHomfold‑LAST: 0.654 Sensitivity RNASampler(20): 0.507 CentroidHomfold‑LAST: 0.524 Positive Predictive Value RNASampler(20): 0.865 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	44 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Sfold: 0.644 Sensitivity CentroidHomfold‑LAST: 0.515 Sfold: 0.549 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Sfold: 0.762 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 6.06606238843e-08	9 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 MXScarna(20): 0.598 Sensitivity CentroidHomfold‑LAST: 0.524 MXScarna(20): 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.822 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	44 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Contrafold: 0.662 Sensitivity CentroidHomfold‑LAST: 0.515 Contrafold: 0.579 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Contrafold: 0.764 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 9.17559933998e-05	44 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Fold: 0.611 Sensitivity CentroidHomfold‑LAST: 0.515 Fold: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Fold: 0.692 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 HotKnots: 0.646 Sensitivity CentroidHomfold‑LAST: 0.515 HotKnots: 0.581 Positive Predictive Value CentroidHomfold‑LAST: 0.873 HotKnots: 0.726 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 4.1569883686e-08		= CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 IPknot: 0.669 Sensitivity CentroidHomfold‑LAST: 0.522 IPknot: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.866 IPknot: 0.796 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.893076023681	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 MaxExpect: 0.613 Sensitivity CentroidHomfold‑LAST: 0.515 MaxExpect: 0.542 Positive Predictive Value CentroidHomfold‑LAST: 0.873 MaxExpect: 0.701 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 UNAFold: 0.616 Sensitivity CentroidHomfold‑LAST: 0.515 UNAFold: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.873 UNAFold: 0.701 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.699 CentroidHomfold‑LAST: 0.645 Sensitivity ContextFold: 0.586 CentroidHomfold‑LAST: 0.502 Positive Predictive Value ContextFold: 0.838 CentroidHomfold‑LAST: 0.836 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAshapes: 0.628 Sensitivity CentroidHomfold‑LAST: 0.515 RNAshapes: 0.555 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAshapes: 0.718 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAfold: 0.635 Sensitivity CentroidHomfold‑LAST: 0.515 RNAfold: 0.562 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAfold: 0.724 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 PknotsRG: 0.641 Sensitivity CentroidHomfold‑LAST: 0.515 PknotsRG: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.873 PknotsRG: 0.723 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 CentroidAlifold(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.501 CentroidAlifold(seed): 0.355 Positive Predictive Value CentroidHomfold‑LAST: 0.808 CentroidAlifold(seed): 0.937 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 ProbKnot: 0.612 Sensitivity CentroidHomfold‑LAST: 0.515 ProbKnot: 0.556 Positive Predictive Value CentroidHomfold‑LAST: 0.873 ProbKnot: 0.680 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Murlet(20): 0.576 Sensitivity CentroidHomfold‑LAST: 0.524 Murlet(20): 0.438 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Carnac(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.524 Carnac(20): 0.341 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 Afold: 0.664 Sensitivity CentroidHomfold‑LAST: 0.542 Afold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.834 Afold: 0.726 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.369701004532	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAsubopt: 0.613 Sensitivity CentroidHomfold‑LAST: 0.515 RNAsubopt: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAsubopt: 0.697 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.663 Cylofold: 0.586 Sensitivity CentroidHomfold‑LAST: 0.487 Cylofold: 0.499 Positive Predictive Value CentroidHomfold‑LAST: 0.909 Cylofold: 0.698 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 McQFold: 0.616 Sensitivity CentroidHomfold‑LAST: 0.515 McQFold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.873 McQFold: 0.723 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.573 RNAalifold(seed): 0.529 Sensitivity CentroidHomfold‑LAST: 0.450 RNAalifold(seed): 0.349 Positive Predictive Value CentroidHomfold‑LAST: 0.736 RNAalifold(seed): 0.808 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Pknots: 0.580 Sensitivity CentroidHomfold‑LAST: 0.515 Pknots: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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: 5.23657817852e-08	? RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.504 CentroidHomfold‑LAST: 0.496 Sensitivity RNASampler(seed): 0.369 CentroidHomfold‑LAST: 0.403 Positive Predictive Value RNASampler(seed): 0.696 CentroidHomfold‑LAST: 0.619 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ 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: 3.56938820447e-08	? CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RSpredict(20): 0.494 Sensitivity CentroidHomfold‑LAST: 0.524 RSpredict(20): 0.376 Positive Predictive Value CentroidHomfold‑LAST: 0.822 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Mastr(20): 0.592 Sensitivity CentroidHomfold‑LAST: 0.524 Mastr(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Vsfold4: 0.548 Sensitivity CentroidHomfold‑LAST: 0.515 Vsfold4: 0.462 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Vsfold4: 0.658 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNASLOpt: 0.581 Sensitivity CentroidHomfold‑LAST: 0.502 RNASLOpt: 0.488 Positive Predictive Value CentroidHomfold‑LAST: 0.836 RNASLOpt: 0.699 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Multilign(20): 0.574 Sensitivity CentroidHomfold‑LAST: 0.524 Multilign(20): 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 RNAwolf: 0.502 Sensitivity CentroidHomfold‑LAST: 0.522 RNAwolf: 0.469 Positive Predictive Value CentroidHomfold‑LAST: 0.866 RNAwolf: 0.546 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.573 Murlet(seed): 0.465 Sensitivity CentroidHomfold‑LAST: 0.450 Murlet(seed): 0.279 Positive Predictive Value CentroidHomfold‑LAST: 0.736 Murlet(seed): 0.780 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 MCFold: 0.567 Sensitivity CentroidHomfold‑LAST: 0.530 MCFold: 0.593 Positive Predictive Value CentroidHomfold‑LAST: 0.863 MCFold: 0.552 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.665 Vsfold5: 0.487 Sensitivity CentroidHomfold‑LAST: 0.511 Vsfold5: 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.872 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.706 RDfolder: 0.538 Sensitivity CentroidHomfold‑LAST: 0.542 RDfolder: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.927 RDfolder: 0.693 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 RSpredict(seed): 0.226 Sensitivity CentroidHomfold‑LAST: 0.501 RSpredict(seed): 0.106 Positive Predictive Value CentroidHomfold‑LAST: 0.808 RSpredict(seed): 0.494 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 PPfold(seed): 0.102 Sensitivity CentroidHomfold‑LAST: 0.479 PPfold(seed): 0.020 Positive Predictive Value CentroidHomfold‑LAST: 0.795 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.07842257011e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.613 NanoFolder: 0.473 Sensitivity CentroidHomfold‑LAST: 0.482 NanoFolder: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.787 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.501 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	? CMfinder(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 Multilign(seed): 0.593 Sensitivity CentroidHomfold‑LAST: 0.481 Multilign(seed): 0.475 Positive Predictive Value CentroidHomfold‑LAST: 0.844 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidHomfold‑LAST: 0.575 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidHomfold‑LAST: 0.453 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidHomfold‑LAST: 0.737 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 TurboFold(20): 0.620 Sensitivity CentroidHomfold‑LAST: 0.524 TurboFold(20): 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.822 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidHomfold‑LAST: 0.581 Sensitivity PETfold_pre2.0(20): 0.497 CentroidHomfold‑LAST: 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidHomfold‑LAST: 0.729 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.593 TurboFold(seed): 0.550 Sensitivity CentroidHomfold‑LAST: 0.470 TurboFold(seed): 0.456 Positive Predictive Value CentroidHomfold‑LAST: 0.756 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.663 CentroidHomfold‑LAST: 0.654 Sensitivity PPfold(20): 0.514 CentroidHomfold‑LAST: 0.524 Positive Predictive Value PPfold(20): 0.861 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.593 Carnac(seed): 0.284 Sensitivity CentroidHomfold‑LAST: 0.470 Carnac(seed): 0.081 Positive Predictive Value CentroidHomfold‑LAST: 0.756 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
IPknot	11 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.624 IPknot: 0.590 Sensitivity MXScarna(seed): 0.493 IPknot: 0.471 Positive Predictive Value MXScarna(seed): 0.796 IPknot: 0.747 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09	38 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.675 CentroidFold: 0.665 Sensitivity IPknot: 0.573 CentroidFold: 0.565 Positive Predictive Value IPknot: 0.801 CentroidFold: 0.789 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 IPknot: 0.571 Sensitivity CentroidAlifold(20): 0.515 IPknot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.933 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.627 IPknot: 0.571 Sensitivity RNAalifold(20): 0.481 IPknot: 0.463 Positive Predictive Value RNAalifold(20): 0.823 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.637 IPknot: 0.571 Sensitivity RNASampler(20): 0.478 IPknot: 0.463 Positive Predictive Value RNASampler(20): 0.854 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.675 Sfold: 0.638 Sensitivity IPknot: 0.573 Sfold: 0.542 Positive Predictive Value IPknot: 0.801 Sfold: 0.758 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.586 IPknot: 0.571 Sensitivity MXScarna(20): 0.474 IPknot: 0.463 Positive Predictive Value MXScarna(20): 0.731 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.675 Contrafold: 0.658 Sensitivity IPknot: 0.573 Contrafold: 0.576 Positive Predictive Value IPknot: 0.801 Contrafold: 0.759 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.675 Fold: 0.611 Sensitivity IPknot: 0.573 Fold: 0.545 Positive Predictive Value IPknot: 0.801 Fold: 0.692 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.675 HotKnots: 0.641 Sensitivity IPknot: 0.573 HotKnots: 0.577 Positive Predictive Value IPknot: 0.801 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 IPknot: 0.669 Sensitivity CentroidHomfold‑LAST: 0.522 IPknot: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.866 IPknot: 0.796 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.893076023681		+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.675 MaxExpect: 0.613 Sensitivity IPknot: 0.573 MaxExpect: 0.541 Positive Predictive Value IPknot: 0.801 MaxExpect: 0.701 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.675 UNAFold: 0.610 Sensitivity IPknot: 0.573 UNAFold: 0.543 Positive Predictive Value IPknot: 0.801 UNAFold: 0.693 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.705 IPknot: 0.665 Sensitivity ContextFold: 0.594 IPknot: 0.568 Positive Predictive Value ContextFold: 0.843 IPknot: 0.785 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.675 RNAshapes: 0.623 Sensitivity IPknot: 0.573 RNAshapes: 0.551 Positive Predictive Value IPknot: 0.801 RNAshapes: 0.711 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.675 RNAfold: 0.628 Sensitivity IPknot: 0.573 RNAfold: 0.556 Positive Predictive Value IPknot: 0.801 RNAfold: 0.717 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.675 PknotsRG: 0.637 Sensitivity IPknot: 0.573 PknotsRG: 0.572 Positive Predictive Value IPknot: 0.801 PknotsRG: 0.716 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	= IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.590 CentroidAlifold(seed): 0.583 Sensitivity IPknot: 0.471 CentroidAlifold(seed): 0.347 Positive Predictive Value IPknot: 0.747 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00654707608169	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.675 ProbKnot: 0.610 Sensitivity IPknot: 0.573 ProbKnot: 0.555 Positive Predictive Value IPknot: 0.801 ProbKnot: 0.679 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.581 IPknot: 0.571 Sensitivity Murlet(20): 0.433 IPknot: 0.463 Positive Predictive Value Murlet(20): 0.785 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.571 Carnac(20): 0.560 Sensitivity IPknot: 0.463 Carnac(20): 0.367 Positive Predictive Value IPknot: 0.710 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.728 Afold: 0.670 Sensitivity IPknot: 0.628 Afold: 0.615 Positive Predictive Value IPknot: 0.848 Afold: 0.738 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.675 RNAsubopt: 0.604 Sensitivity IPknot: 0.573 RNAsubopt: 0.538 Positive Predictive Value IPknot: 0.801 RNAsubopt: 0.686 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.669 Cylofold: 0.583 Sensitivity IPknot: 0.559 Cylofold: 0.498 Positive Predictive Value IPknot: 0.809 Cylofold: 0.692 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.669 McQFold: 0.604 Sensitivity IPknot: 0.567 McQFold: 0.522 Positive Predictive Value IPknot: 0.796 McQFold: 0.707 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.523 IPknot: 0.505 Sensitivity RNAalifold(seed): 0.344 IPknot: 0.402 Positive Predictive Value RNAalifold(seed): 0.800 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.675 Pknots: 0.574 Sensitivity IPknot: 0.573 Pknots: 0.516 Positive Predictive Value IPknot: 0.801 Pknots: 0.646 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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: 5.1503931209e-08	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.493 RNASampler(seed): 0.471 Sensitivity IPknot: 0.395 RNASampler(seed): 0.341 Positive Predictive Value IPknot: 0.622 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ 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 RSpredict(20) Matthews Correlation Coefficient IPknot: 0.571 RSpredict(20): 0.489 Sensitivity IPknot: 0.463 RSpredict(20): 0.367 Positive Predictive Value IPknot: 0.710 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.571 Mastr(20): 0.567 Sensitivity IPknot: 0.463 Mastr(20): 0.389 Positive Predictive Value IPknot: 0.710 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.675 Vsfold4: 0.537 Sensitivity IPknot: 0.573 Vsfold4: 0.458 Positive Predictive Value IPknot: 0.801 Vsfold4: 0.639 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.665 RNASLOpt: 0.591 Sensitivity IPknot: 0.568 RNASLOpt: 0.498 Positive Predictive Value IPknot: 0.785 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.571 Multilign(20): 0.540 Sensitivity IPknot: 0.463 Multilign(20): 0.456 Positive Predictive Value IPknot: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.675 RNAwolf: 0.512 Sensitivity IPknot: 0.573 RNAwolf: 0.479 Positive Predictive Value IPknot: 0.801 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.505 Murlet(seed): 0.451 Sensitivity IPknot: 0.402 Murlet(seed): 0.268 Positive Predictive Value IPknot: 0.641 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.688 MCFold: 0.571 Sensitivity IPknot: 0.589 MCFold: 0.599 Positive Predictive Value IPknot: 0.808 MCFold: 0.552 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.672 Vsfold5: 0.479 Sensitivity IPknot: 0.570 Vsfold5: 0.420 Positive Predictive Value IPknot: 0.799 Vsfold5: 0.557 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.659 RDfolder: 0.496 Sensitivity IPknot: 0.550 RDfolder: 0.388 Positive Predictive Value IPknot: 0.799 RDfolder: 0.647 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.590 RSpredict(seed): 0.193 Sensitivity IPknot: 0.471 RSpredict(seed): 0.084 Positive Predictive Value IPknot: 0.747 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.25253056981e-08	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.590 PPfold(seed): 0.102 Sensitivity IPknot: 0.471 PPfold(seed): 0.020 Positive Predictive Value IPknot: 0.747 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.678 NanoFolder: 0.490 Sensitivity IPknot: 0.576 NanoFolder: 0.495 Positive Predictive Value IPknot: 0.804 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.590 Mastr(seed): 0.000 Sensitivity IPknot: 0.471 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.62909925123e-09	? 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	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.560 Multilign(seed): 0.538 Sensitivity IPknot: 0.435 Multilign(seed): 0.420 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 IPknot: 0.551 Sensitivity PETfold_pre2.0(seed): 0.551 IPknot: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.594 IPknot: 0.571 Sensitivity TurboFold(20): 0.470 IPknot: 0.463 Positive Predictive Value TurboFold(20): 0.756 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 IPknot: 0.502 Sensitivity PETfold_pre2.0(20): 0.497 IPknot: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.544 TurboFold(seed): 0.517 Sensitivity IPknot: 0.437 TurboFold(seed): 0.422 Positive Predictive Value IPknot: 0.685 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.665 IPknot: 0.571 Sensitivity PPfold(20): 0.519 IPknot: 0.463 Positive Predictive Value PPfold(20): 0.859 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.544 Carnac(seed): 0.123 Sensitivity IPknot: 0.437 Carnac(seed): 0.015 Positive Predictive Value IPknot: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
MaxExpect	40 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.667 MaxExpect: 0.605 Sensitivity MXScarna(seed): 0.557 MaxExpect: 0.543 Positive Predictive Value MXScarna(seed): 0.801 MaxExpect: 0.677 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.631 MaxExpect: 0.617 Sensitivity CentroidFold: 0.530 MaxExpect: 0.540 Positive Predictive Value CentroidFold: 0.754 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.680 MaxExpect: 0.588 Sensitivity CentroidAlifold(20): 0.520 MaxExpect: 0.516 Positive Predictive Value CentroidAlifold(20): 0.892 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.642 MaxExpect: 0.588 Sensitivity RNAalifold(20): 0.492 MaxExpect: 0.516 Positive Predictive Value RNAalifold(20): 0.842 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.636 MaxExpect: 0.588 Sensitivity RNASampler(20): 0.484 MaxExpect: 0.516 Positive Predictive Value RNASampler(20): 0.840 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	99 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.617 Sfold: 0.595 Sensitivity MaxExpect: 0.540 Sfold: 0.501 Positive Predictive Value MaxExpect: 0.705 Sfold: 0.707 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.21776328505e-08	26 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.630 MaxExpect: 0.588 Sensitivity MXScarna(20): 0.526 MaxExpect: 0.516 Positive Predictive Value MXScarna(20): 0.758 MaxExpect: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	99 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.626 MaxExpect: 0.617 Sensitivity Contrafold: 0.551 MaxExpect: 0.540 Positive Predictive Value Contrafold: 0.712 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.21776328505e-08	82 Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.679 MaxExpect: 0.665 Sensitivity Fold: 0.618 MaxExpect: 0.601 Positive Predictive Value Fold: 0.751 MaxExpect: 0.740 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.62644058675e-08	98 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.661 MaxExpect: 0.653 Sensitivity HotKnots: 0.602 MaxExpect: 0.587 Positive Predictive Value HotKnots: 0.729 MaxExpect: 0.731 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 MaxExpect: 0.613 Sensitivity CentroidHomfold‑LAST: 0.515 MaxExpect: 0.542 Positive Predictive Value CentroidHomfold‑LAST: 0.873 MaxExpect: 0.701 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.675 MaxExpect: 0.613 Sensitivity IPknot: 0.573 MaxExpect: 0.541 Positive Predictive Value IPknot: 0.801 MaxExpect: 0.701 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.617 UNAFold: 0.580 Sensitivity MaxExpect: 0.540 UNAFold: 0.511 Positive Predictive Value MaxExpect: 0.705 UNAFold: 0.659 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08	- ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.705 MaxExpect: 0.608 Sensitivity ContextFold: 0.594 MaxExpect: 0.536 Positive Predictive Value ContextFold: 0.843 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.653 RNAshapes: 0.653 Sensitivity MaxExpect: 0.587 RNAshapes: 0.587 Positive Predictive Value MaxExpect: 0.731 RNAshapes: 0.731 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.0655545093322	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.617 RNAfold: 0.571 Sensitivity MaxExpect: 0.540 RNAfold: 0.507 Positive Predictive Value MaxExpect: 0.705 RNAfold: 0.642 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.617 PknotsRG: 0.559 Sensitivity MaxExpect: 0.540 PknotsRG: 0.499 Positive Predictive Value MaxExpect: 0.705 PknotsRG: 0.628 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 MaxExpect: 0.605 Sensitivity CentroidAlifold(seed): 0.422 MaxExpect: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.877 MaxExpect: 0.677 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.0024921586113	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.653 ProbKnot: 0.646 Sensitivity MaxExpect: 0.590 ProbKnot: 0.597 Positive Predictive Value MaxExpect: 0.728 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.588 Murlet(20): 0.581 Sensitivity MaxExpect: 0.516 Murlet(20): 0.425 Positive Predictive Value MaxExpect: 0.675 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 9.71546425945e-06	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.588 Carnac(20): 0.584 Sensitivity MaxExpect: 0.516 Carnac(20): 0.375 Positive Predictive Value MaxExpect: 0.675 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.61414169632e-05	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.611 Afold: 0.564 Sensitivity MaxExpect: 0.538 Afold: 0.505 Positive Predictive Value MaxExpect: 0.695 Afold: 0.630 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.653 RNAsubopt: 0.640 Sensitivity MaxExpect: 0.587 RNAsubopt: 0.581 Positive Predictive Value MaxExpect: 0.731 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.690 Cylofold: 0.648 Sensitivity MaxExpect: 0.616 Cylofold: 0.559 Positive Predictive Value MaxExpect: 0.778 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.615 McQFold: 0.519 Sensitivity MaxExpect: 0.538 McQFold: 0.445 Positive Predictive Value MaxExpect: 0.704 McQFold: 0.606 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.588 MaxExpect: 0.584 Sensitivity RNAalifold(seed): 0.394 MaxExpect: 0.529 Positive Predictive Value RNAalifold(seed): 0.881 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.14339240505	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.678 Pknots: 0.635 Sensitivity MaxExpect: 0.606 Pknots: 0.579 Positive Predictive Value MaxExpect: 0.765 Pknots: 0.704 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-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	- RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.662 MaxExpect: 0.646 Sensitivity RNASampler(seed): 0.529 MaxExpect: 0.599 Positive Predictive Value RNASampler(seed): 0.835 MaxExpect: 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.78784325942e-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: 0.000524630860266	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.588 RSpredict(20): 0.543 Sensitivity MaxExpect: 0.516 RSpredict(20): 0.425 Positive Predictive Value MaxExpect: 0.675 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.588 Mastr(20): 0.521 Sensitivity MaxExpect: 0.516 Mastr(20): 0.342 Positive Predictive Value MaxExpect: 0.675 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.653 Vsfold4: 0.560 Sensitivity MaxExpect: 0.587 Vsfold4: 0.480 Positive Predictive Value MaxExpect: 0.731 Vsfold4: 0.657 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.608 RNASLOpt: 0.591 Sensitivity MaxExpect: 0.536 RNASLOpt: 0.498 Positive Predictive Value MaxExpect: 0.696 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.18450348589e-07	+ MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.531 Multilign(20): 0.521 Sensitivity MaxExpect: 0.464 Multilign(20): 0.428 Positive Predictive Value MaxExpect: 0.616 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.08077114986e-06	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.613 RNAwolf: 0.512 Sensitivity MaxExpect: 0.541 RNAwolf: 0.479 Positive Predictive Value MaxExpect: 0.701 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.630 Murlet(seed): 0.538 Sensitivity MaxExpect: 0.561 Murlet(seed): 0.339 Positive Predictive Value MaxExpect: 0.713 Murlet(seed): 0.862 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.676 MCFold: 0.557 Sensitivity MaxExpect: 0.608 MCFold: 0.580 Positive Predictive Value MaxExpect: 0.758 MCFold: 0.543 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.652 Vsfold5: 0.519 Sensitivity MaxExpect: 0.586 Vsfold5: 0.451 Positive Predictive Value MaxExpect: 0.730 Vsfold5: 0.604 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.703 RDfolder: 0.590 Sensitivity MaxExpect: 0.627 RDfolder: 0.490 Positive Predictive Value MaxExpect: 0.796 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.605 RSpredict(seed): 0.306 Sensitivity MaxExpect: 0.543 RSpredict(seed): 0.156 Positive Predictive Value MaxExpect: 0.677 RSpredict(seed): 0.607 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.513 PPfold(seed): 0.102 Sensitivity MaxExpect: 0.434 PPfold(seed): 0.020 Positive Predictive Value MaxExpect: 0.615 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.601 NanoFolder: 0.490 Sensitivity MaxExpect: 0.530 NanoFolder: 0.495 Positive Predictive Value MaxExpect: 0.689 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.605 Mastr(seed): 0.273 Sensitivity MaxExpect: 0.543 Mastr(seed): 0.083 Positive Predictive Value MaxExpect: 0.677 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 40 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	? Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.593 MaxExpect: 0.575 Sensitivity Multilign(seed): 0.475 MaxExpect: 0.481 Positive Predictive Value Multilign(seed): 0.750 MaxExpect: 0.697 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MaxExpect: 0.458 Sensitivity PETfold_pre2.0(seed): 0.551 MaxExpect: 0.390 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.620 MaxExpect: 0.577 Sensitivity TurboFold(20): 0.500 MaxExpect: 0.497 Positive Predictive Value TurboFold(20): 0.775 MaxExpect: 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MaxExpect: 0.479 Sensitivity PETfold_pre2.0(20): 0.497 MaxExpect: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.550 MaxExpect: 0.528 Sensitivity TurboFold(seed): 0.456 MaxExpect: 0.452 Positive Predictive Value TurboFold(seed): 0.672 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.663 MaxExpect: 0.577 Sensitivity PPfold(20): 0.514 MaxExpect: 0.497 Positive Predictive Value PPfold(20): 0.861 MaxExpect: 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.643 Carnac(seed): 0.245 Sensitivity MaxExpect: 0.575 Carnac(seed): 0.061 Positive Predictive Value MaxExpect: 0.725 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08
UNAFold	44 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.673 UNAFold: 0.599 Sensitivity MXScarna(seed): 0.562 UNAFold: 0.540 Positive Predictive Value MXScarna(seed): 0.809 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.577 UNAFold: 0.526 Sensitivity CentroidFold: 0.493 UNAFold: 0.476 Positive Predictive Value CentroidFold: 0.676 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 UNAFold: 0.585 Sensitivity CentroidAlifold(20): 0.520 UNAFold: 0.515 Positive Predictive Value CentroidAlifold(20): 0.892 UNAFold: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.644 UNAFold: 0.585 Sensitivity RNAalifold(20): 0.491 UNAFold: 0.512 Positive Predictive Value RNAalifold(20): 0.849 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.634 UNAFold: 0.585 Sensitivity RNASampler(20): 0.477 UNAFold: 0.512 Positive Predictive Value RNASampler(20): 0.844 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	121 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.527 UNAFold: 0.508 Sensitivity Sfold: 0.448 UNAFold: 0.454 Positive Predictive Value Sfold: 0.621 UNAFold: 0.569 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.628 UNAFold: 0.585 Sensitivity MXScarna(20): 0.523 UNAFold: 0.512 Positive Predictive Value MXScarna(20): 0.757 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	121 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.575 UNAFold: 0.508 Sensitivity Contrafold: 0.511 UNAFold: 0.454 Positive Predictive Value Contrafold: 0.648 UNAFold: 0.569 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.679 UNAFold: 0.670 Sensitivity Fold: 0.618 UNAFold: 0.608 Positive Predictive Value Fold: 0.751 UNAFold: 0.743 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 2.82781450476e-07	118 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.664 HotKnots: 0.662 Sensitivity UNAFold: 0.595 HotKnots: 0.600 Positive Predictive Value UNAFold: 0.747 HotKnots: 0.736 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.64686539471e-05	44 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 UNAFold: 0.616 Sensitivity CentroidHomfold‑LAST: 0.515 UNAFold: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.873 UNAFold: 0.701 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.675 UNAFold: 0.610 Sensitivity IPknot: 0.573 UNAFold: 0.543 Positive Predictive Value IPknot: 0.801 UNAFold: 0.693 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.617 UNAFold: 0.580 Sensitivity MaxExpect: 0.540 UNAFold: 0.511 Positive Predictive Value MaxExpect: 0.705 UNAFold: 0.659 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08		- ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.705 UNAFold: 0.600 Sensitivity ContextFold: 0.594 UNAFold: 0.538 Positive Predictive Value ContextFold: 0.843 UNAFold: 0.676 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.664 RNAshapes: 0.650 Sensitivity UNAFold: 0.595 RNAshapes: 0.580 Positive Predictive Value UNAFold: 0.747 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.508 RNAfold: 0.504 Sensitivity UNAFold: 0.454 RNAfold: 0.454 Positive Predictive Value UNAFold: 0.569 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.508 PknotsRG: 0.495 Sensitivity UNAFold: 0.454 PknotsRG: 0.447 Positive Predictive Value UNAFold: 0.569 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 UNAFold: 0.596 Sensitivity CentroidAlifold(seed): 0.419 UNAFold: 0.537 Positive Predictive Value CentroidAlifold(seed): 0.878 UNAFold: 0.665 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 1.59851305843e-05	+ UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.650 ProbKnot: 0.646 Sensitivity UNAFold: 0.589 ProbKnot: 0.597 Positive Predictive Value UNAFold: 0.721 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.5875416339e-07	= UNAFold vs Murlet(20) Matthews Correlation Coefficient UNAFold: 0.585 Murlet(20): 0.582 Sensitivity UNAFold: 0.512 Murlet(20): 0.423 Positive Predictive Value UNAFold: 0.672 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0414928403863	= UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.585 Carnac(20): 0.582 Sensitivity UNAFold: 0.512 Carnac(20): 0.371 Positive Predictive Value UNAFold: 0.672 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0014549156141	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.495 Afold: 0.491 Sensitivity UNAFold: 0.444 Afold: 0.446 Positive Predictive Value UNAFold: 0.551 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 2.23046259944e-06	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.664 RNAsubopt: 0.635 Sensitivity UNAFold: 0.595 RNAsubopt: 0.574 Positive Predictive Value UNAFold: 0.747 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.685 Cylofold: 0.648 Sensitivity UNAFold: 0.612 Cylofold: 0.559 Positive Predictive Value UNAFold: 0.772 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.507 McQFold: 0.443 Sensitivity UNAFold: 0.453 McQFold: 0.348 Positive Predictive Value UNAFold: 0.568 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.609 RNAalifold(seed): 0.593 Sensitivity UNAFold: 0.551 RNAalifold(seed): 0.397 Positive Predictive Value UNAFold: 0.675 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.688 Pknots: 0.634 Sensitivity UNAFold: 0.612 Pknots: 0.575 Positive Predictive Value UNAFold: 0.780 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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 RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.690 RNASampler(seed): 0.673 Sensitivity UNAFold: 0.635 RNASampler(seed): 0.535 Positive Predictive Value UNAFold: 0.754 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ 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: 8.62431444312e-06	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.589 RSpredict(20): 0.547 Sensitivity UNAFold: 0.519 RSpredict(20): 0.428 Positive Predictive Value UNAFold: 0.673 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.585 Mastr(20): 0.525 Sensitivity UNAFold: 0.512 Mastr(20): 0.346 Positive Predictive Value UNAFold: 0.672 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.664 Vsfold4: 0.562 Sensitivity UNAFold: 0.595 Vsfold4: 0.481 Positive Predictive Value UNAFold: 0.747 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	= UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.600 RNASLOpt: 0.591 Sensitivity UNAFold: 0.538 RNASLOpt: 0.498 Positive Predictive Value UNAFold: 0.676 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.00151316827629	+ UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.557 Multilign(20): 0.521 Sensitivity UNAFold: 0.482 Multilign(20): 0.428 Positive Predictive Value UNAFold: 0.650 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.610 RNAwolf: 0.512 Sensitivity UNAFold: 0.543 RNAwolf: 0.479 Positive Predictive Value UNAFold: 0.693 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.663 Murlet(seed): 0.539 Sensitivity UNAFold: 0.586 Murlet(seed): 0.337 Positive Predictive Value UNAFold: 0.754 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.700 MCFold: 0.577 Sensitivity UNAFold: 0.628 MCFold: 0.597 Positive Predictive Value UNAFold: 0.787 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.663 Vsfold5: 0.528 Sensitivity UNAFold: 0.594 Vsfold5: 0.458 Positive Predictive Value UNAFold: 0.746 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.719 RDfolder: 0.596 Sensitivity UNAFold: 0.639 RDfolder: 0.495 Positive Predictive Value UNAFold: 0.817 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.599 RSpredict(seed): 0.314 Sensitivity UNAFold: 0.540 RSpredict(seed): 0.161 Positive Predictive Value UNAFold: 0.667 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.490 PPfold(seed): 0.102 Sensitivity UNAFold: 0.417 PPfold(seed): 0.020 Positive Predictive Value UNAFold: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.576 NanoFolder: 0.490 Sensitivity UNAFold: 0.515 NanoFolder: 0.495 Positive Predictive Value UNAFold: 0.653 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.595 Mastr(seed): 0.258 Sensitivity UNAFold: 0.534 Mastr(seed): 0.075 Positive Predictive Value UNAFold: 0.667 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.593 UNAFold: 0.590 Sensitivity Multilign(seed): 0.475 UNAFold: 0.494 Positive Predictive Value Multilign(seed): 0.750 UNAFold: 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 UNAFold: 0.413 Sensitivity PETfold_pre2.0(seed): 0.551 UNAFold: 0.358 Positive Predictive Value PETfold_pre2.0(seed): 0.843 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.620 UNAFold: 0.589 Sensitivity TurboFold(20): 0.500 UNAFold: 0.507 Positive Predictive Value TurboFold(20): 0.775 UNAFold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 UNAFold: 0.478 Sensitivity PETfold_pre2.0(20): 0.497 UNAFold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 UNAFold: 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.550 UNAFold: 0.535 Sensitivity TurboFold(seed): 0.456 UNAFold: 0.463 Positive Predictive Value TurboFold(seed): 0.672 UNAFold: 0.627 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.663 UNAFold: 0.589 Sensitivity PPfold(20): 0.514 UNAFold: 0.507 Positive Predictive Value PPfold(20): 0.861 UNAFold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.666 Carnac(seed): 0.260 Sensitivity UNAFold: 0.594 Carnac(seed): 0.068 Positive Predictive Value UNAFold: 0.752 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
ContextFold	8 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.616 MXScarna(seed): 0.586 Sensitivity ContextFold: 0.476 MXScarna(seed): 0.457 Positive Predictive Value ContextFold: 0.801 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	30 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.705 CentroidFold: 0.654 Sensitivity ContextFold: 0.594 CentroidFold: 0.556 Positive Predictive Value ContextFold: 0.843 CentroidFold: 0.775 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.650 ContextFold: 0.579 Sensitivity CentroidAlifold(20): 0.473 ContextFold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.898 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.579 RNAalifold(20): 0.553 Sensitivity ContextFold: 0.443 RNAalifold(20): 0.407 Positive Predictive Value ContextFold: 0.763 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.579 RNASampler(20): 0.569 Sensitivity ContextFold: 0.443 RNASampler(20): 0.419 Positive Predictive Value ContextFold: 0.763 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.705 Sfold: 0.629 Sensitivity ContextFold: 0.594 Sfold: 0.536 Positive Predictive Value ContextFold: 0.843 Sfold: 0.744 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.579 MXScarna(20): 0.501 Sensitivity ContextFold: 0.443 MXScarna(20): 0.401 Positive Predictive Value ContextFold: 0.763 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.705 Contrafold: 0.649 Sensitivity ContextFold: 0.594 Contrafold: 0.568 Positive Predictive Value ContextFold: 0.843 Contrafold: 0.749 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.705 Fold: 0.609 Sensitivity ContextFold: 0.594 Fold: 0.543 Positive Predictive Value ContextFold: 0.843 Fold: 0.690 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.705 HotKnots: 0.638 Sensitivity ContextFold: 0.594 HotKnots: 0.579 Positive Predictive Value ContextFold: 0.843 HotKnots: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	29 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.699 CentroidHomfold‑LAST: 0.645 Sensitivity ContextFold: 0.586 CentroidHomfold‑LAST: 0.502 Positive Predictive Value ContextFold: 0.838 CentroidHomfold‑LAST: 0.836 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	30 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.705 IPknot: 0.665 Sensitivity ContextFold: 0.594 IPknot: 0.568 Positive Predictive Value ContextFold: 0.843 IPknot: 0.785 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.705 MaxExpect: 0.608 Sensitivity ContextFold: 0.594 MaxExpect: 0.536 Positive Predictive Value ContextFold: 0.843 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.705 UNAFold: 0.600 Sensitivity ContextFold: 0.594 UNAFold: 0.538 Positive Predictive Value ContextFold: 0.843 UNAFold: 0.676 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.705 RNAshapes: 0.617 Sensitivity ContextFold: 0.594 RNAshapes: 0.548 Positive Predictive Value ContextFold: 0.843 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.705 RNAfold: 0.624 Sensitivity ContextFold: 0.594 RNAfold: 0.554 Positive Predictive Value ContextFold: 0.843 RNAfold: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.705 PknotsRG: 0.637 Sensitivity ContextFold: 0.594 PknotsRG: 0.574 Positive Predictive Value ContextFold: 0.843 PknotsRG: 0.713 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.616 CentroidAlifold(seed): 0.542 Sensitivity ContextFold: 0.476 CentroidAlifold(seed): 0.299 Positive Predictive Value ContextFold: 0.801 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.705 ProbKnot: 0.611 Sensitivity ContextFold: 0.594 ProbKnot: 0.558 Positive Predictive Value ContextFold: 0.843 ProbKnot: 0.676 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.579 Murlet(20): 0.496 Sensitivity ContextFold: 0.443 Murlet(20): 0.353 Positive Predictive Value ContextFold: 0.763 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.579 Carnac(20): 0.476 Sensitivity ContextFold: 0.443 Carnac(20): 0.281 Positive Predictive Value ContextFold: 0.763 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.709 Afold: 0.677 Sensitivity ContextFold: 0.610 Afold: 0.624 Positive Predictive Value ContextFold: 0.831 Afold: 0.740 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.67407019774e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.705 RNAsubopt: 0.584 Sensitivity ContextFold: 0.594 RNAsubopt: 0.525 Positive Predictive Value ContextFold: 0.843 RNAsubopt: 0.658 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.703 Cylofold: 0.578 Sensitivity ContextFold: 0.591 Cylofold: 0.494 Positive Predictive Value ContextFold: 0.842 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.699 McQFold: 0.578 Sensitivity ContextFold: 0.586 McQFold: 0.505 Positive Predictive Value ContextFold: 0.838 McQFold: 0.670 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.488 RNAalifold(seed): 0.472 Sensitivity ContextFold: 0.376 RNAalifold(seed): 0.293 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.705 Pknots: 0.547 Sensitivity ContextFold: 0.594 Pknots: 0.497 Positive Predictive Value ContextFold: 0.843 Pknots: 0.611 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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: 2.24270395587e-08	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.351 RNASampler(seed): 0.198 Sensitivity ContextFold: 0.283 RNASampler(seed): 0.151 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ 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: 5.19332990918e-08	? ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.579 RSpredict(20): 0.352 Sensitivity ContextFold: 0.443 RSpredict(20): 0.251 Positive Predictive Value ContextFold: 0.763 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.579 Mastr(20): 0.488 Sensitivity ContextFold: 0.443 Mastr(20): 0.305 Positive Predictive Value ContextFold: 0.763 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.705 Vsfold4: 0.537 Sensitivity ContextFold: 0.594 Vsfold4: 0.457 Positive Predictive Value ContextFold: 0.843 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.705 RNASLOpt: 0.591 Sensitivity ContextFold: 0.594 RNASLOpt: 0.498 Positive Predictive Value ContextFold: 0.843 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.579 Multilign(20): 0.474 Sensitivity ContextFold: 0.443 Multilign(20): 0.401 Positive Predictive Value ContextFold: 0.763 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.705 RNAwolf: 0.488 Sensitivity ContextFold: 0.594 RNAwolf: 0.457 Positive Predictive Value ContextFold: 0.843 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.488 Murlet(seed): 0.425 Sensitivity ContextFold: 0.376 Murlet(seed): 0.248 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.719 MCFold: 0.596 Sensitivity ContextFold: 0.613 MCFold: 0.626 Positive Predictive Value ContextFold: 0.848 MCFold: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.704 Vsfold5: 0.468 Sensitivity ContextFold: 0.592 Vsfold5: 0.408 Positive Predictive Value ContextFold: 0.842 Vsfold5: 0.545 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.669 RDfolder: 0.481 Sensitivity ContextFold: 0.561 RDfolder: 0.379 Positive Predictive Value ContextFold: 0.807 RDfolder: 0.623 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	? ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.616 RSpredict(seed): 0.110 Sensitivity ContextFold: 0.476 RSpredict(seed): 0.047 Positive Predictive Value ContextFold: 0.801 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.616 PPfold(seed): 0.121 Sensitivity ContextFold: 0.476 PPfold(seed): 0.028 Positive Predictive Value ContextFold: 0.801 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.706 NanoFolder: 0.490 Sensitivity ContextFold: 0.584 NanoFolder: 0.495 Positive Predictive Value ContextFold: 0.859 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	? ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.616 Mastr(seed): 0.000 Sensitivity ContextFold: 0.476 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.801 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.532 Multilign(seed): 0.403 Sensitivity ContextFold: 0.435 Multilign(seed): 0.306 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ContextFold: 0.616 Sensitivity PETfold_pre2.0(seed): 0.551 ContextFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ContextFold: 0.801 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.579 TurboFold(20): 0.542 Sensitivity ContextFold: 0.443 TurboFold(20): 0.425 Positive Predictive Value ContextFold: 0.763 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ContextFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.497 ContextFold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.576 TurboFold(seed): 0.460 Sensitivity ContextFold: 0.449 TurboFold(seed): 0.380 Positive Predictive Value ContextFold: 0.743 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.616 ContextFold: 0.579 Sensitivity PPfold(20): 0.473 ContextFold: 0.443 Positive Predictive Value PPfold(20): 0.806 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.576 Carnac(seed): 0.146 Sensitivity ContextFold: 0.449 Carnac(seed): 0.021 Positive Predictive Value ContextFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
RNAshapes	44 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAshapes: 0.597 Sensitivity MXScarna(seed): 0.562 RNAshapes: 0.537 Positive Predictive Value MXScarna(seed): 0.809 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.676 RNAshapes: 0.650 Sensitivity CentroidFold: 0.591 RNAshapes: 0.584 Positive Predictive Value CentroidFold: 0.777 RNAshapes: 0.728 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAshapes: 0.582 Sensitivity CentroidAlifold(20): 0.520 RNAshapes: 0.512 Positive Predictive Value CentroidAlifold(20): 0.892 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAshapes: 0.577 Sensitivity RNAalifold(20): 0.491 RNAshapes: 0.506 Positive Predictive Value RNAalifold(20): 0.849 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.634 RNAshapes: 0.577 Sensitivity RNASampler(20): 0.477 RNAshapes: 0.506 Positive Predictive Value RNASampler(20): 0.844 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	118 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.669 RNAshapes: 0.650 Sensitivity Sfold: 0.581 RNAshapes: 0.580 Positive Predictive Value Sfold: 0.775 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.628 RNAshapes: 0.577 Sensitivity MXScarna(20): 0.523 RNAshapes: 0.506 Positive Predictive Value MXScarna(20): 0.757 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	118 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.660 RNAshapes: 0.650 Sensitivity Contrafold: 0.592 RNAshapes: 0.580 Positive Predictive Value Contrafold: 0.740 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.679 RNAshapes: 0.671 Sensitivity Fold: 0.618 RNAshapes: 0.606 Positive Predictive Value Fold: 0.751 RNAshapes: 0.746 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.662 RNAshapes: 0.650 Sensitivity HotKnots: 0.600 RNAshapes: 0.580 Positive Predictive Value HotKnots: 0.736 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAshapes: 0.628 Sensitivity CentroidHomfold‑LAST: 0.515 RNAshapes: 0.555 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAshapes: 0.718 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.675 RNAshapes: 0.623 Sensitivity IPknot: 0.573 RNAshapes: 0.551 Positive Predictive Value IPknot: 0.801 RNAshapes: 0.711 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.653 RNAshapes: 0.653 Sensitivity MaxExpect: 0.587 RNAshapes: 0.587 Positive Predictive Value MaxExpect: 0.731 RNAshapes: 0.731 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.0655545093322	118 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.664 RNAshapes: 0.650 Sensitivity UNAFold: 0.595 RNAshapes: 0.580 Positive Predictive Value UNAFold: 0.747 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.705 RNAshapes: 0.617 Sensitivity ContextFold: 0.594 RNAshapes: 0.548 Positive Predictive Value ContextFold: 0.843 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08		= RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.651 RNAshapes: 0.650 Sensitivity RNAfold: 0.587 RNAshapes: 0.580 Positive Predictive Value RNAfold: 0.726 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.27038065226	+ RNAshapes vs PknotsRG Matthews Correlation Coefficient RNAshapes: 0.650 PknotsRG: 0.646 Sensitivity RNAshapes: 0.580 PknotsRG: 0.585 Positive Predictive Value RNAshapes: 0.733 PknotsRG: 0.718 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 2.91197157422e-05	- CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAshapes: 0.595 Sensitivity CentroidAlifold(seed): 0.419 RNAshapes: 0.535 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 2.71856013146e-06	+ RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.653 ProbKnot: 0.646 Sensitivity RNAshapes: 0.589 ProbKnot: 0.597 Positive Predictive Value RNAshapes: 0.728 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.000114481332584	= Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.582 RNAshapes: 0.577 Sensitivity Murlet(20): 0.423 RNAshapes: 0.506 Positive Predictive Value Murlet(20): 0.804 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0440733078056	- Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.582 RNAshapes: 0.577 Sensitivity Carnac(20): 0.371 RNAshapes: 0.506 Positive Predictive Value Carnac(20): 0.915 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000279205044453	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.659 Afold: 0.647 Sensitivity RNAshapes: 0.596 Afold: 0.595 Positive Predictive Value RNAshapes: 0.733 Afold: 0.709 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.650 RNAsubopt: 0.635 Sensitivity RNAshapes: 0.580 RNAsubopt: 0.574 Positive Predictive Value RNAshapes: 0.733 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.689 Cylofold: 0.648 Sensitivity RNAshapes: 0.614 Cylofold: 0.559 Positive Predictive Value RNAshapes: 0.779 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.648 McQFold: 0.620 Sensitivity RNAshapes: 0.579 McQFold: 0.540 Positive Predictive Value RNAshapes: 0.731 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.627 RNAalifold(seed): 0.593 Sensitivity RNAshapes: 0.567 RNAalifold(seed): 0.397 Positive Predictive Value RNAshapes: 0.696 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.674 Pknots: 0.634 Sensitivity RNAshapes: 0.598 Pknots: 0.575 Positive Predictive Value RNAshapes: 0.765 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-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 RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.696 RNASampler(seed): 0.673 Sensitivity RNAshapes: 0.641 RNASampler(seed): 0.535 Positive Predictive Value RNAshapes: 0.760 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.21817282663e-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: 2.28033735003e-07	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.586 RSpredict(20): 0.547 Sensitivity RNAshapes: 0.516 RSpredict(20): 0.428 Positive Predictive Value RNAshapes: 0.670 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.577 Mastr(20): 0.525 Sensitivity RNAshapes: 0.506 Mastr(20): 0.346 Positive Predictive Value RNAshapes: 0.664 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.650 Vsfold4: 0.562 Sensitivity RNAshapes: 0.580 Vsfold4: 0.481 Positive Predictive Value RNAshapes: 0.733 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.617 RNASLOpt: 0.591 Sensitivity RNAshapes: 0.548 RNASLOpt: 0.498 Positive Predictive Value RNAshapes: 0.702 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.633 Multilign(20): 0.521 Sensitivity RNAshapes: 0.548 Multilign(20): 0.428 Positive Predictive Value RNAshapes: 0.737 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.623 RNAwolf: 0.512 Sensitivity RNAshapes: 0.551 RNAwolf: 0.479 Positive Predictive Value RNAshapes: 0.711 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.692 Murlet(seed): 0.539 Sensitivity RNAshapes: 0.614 Murlet(seed): 0.337 Positive Predictive Value RNAshapes: 0.783 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.692 MCFold: 0.577 Sensitivity RNAshapes: 0.619 MCFold: 0.597 Positive Predictive Value RNAshapes: 0.780 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.649 Vsfold5: 0.528 Sensitivity RNAshapes: 0.580 Vsfold5: 0.458 Positive Predictive Value RNAshapes: 0.732 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.698 RDfolder: 0.596 Sensitivity RNAshapes: 0.617 RDfolder: 0.495 Positive Predictive Value RNAshapes: 0.797 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.597 RSpredict(seed): 0.314 Sensitivity RNAshapes: 0.537 RSpredict(seed): 0.161 Positive Predictive Value RNAshapes: 0.668 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.537 PPfold(seed): 0.102 Sensitivity RNAshapes: 0.454 PPfold(seed): 0.020 Positive Predictive Value RNAshapes: 0.643 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.616 NanoFolder: 0.490 Sensitivity RNAshapes: 0.547 NanoFolder: 0.495 Positive Predictive Value RNAshapes: 0.700 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.591 Mastr(seed): 0.258 Sensitivity RNAshapes: 0.529 Mastr(seed): 0.075 Positive Predictive Value RNAshapes: 0.664 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.672 Multilign(seed): 0.593 Sensitivity RNAshapes: 0.563 Multilign(seed): 0.475 Positive Predictive Value RNAshapes: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAshapes: 0.476 Sensitivity PETfold_pre2.0(seed): 0.551 RNAshapes: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAshapes: 0.562 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.620 RNAshapes: 0.587 Sensitivity TurboFold(20): 0.500 RNAshapes: 0.503 Positive Predictive Value TurboFold(20): 0.775 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAshapes: 0.475 Sensitivity PETfold_pre2.0(20): 0.497 RNAshapes: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAshapes: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.578 TurboFold(seed): 0.550 Sensitivity RNAshapes: 0.498 TurboFold(seed): 0.456 Positive Predictive Value RNAshapes: 0.678 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.663 RNAshapes: 0.587 Sensitivity PPfold(20): 0.514 RNAshapes: 0.503 Positive Predictive Value PPfold(20): 0.861 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.679 Carnac(seed): 0.260 Sensitivity RNAshapes: 0.607 Carnac(seed): 0.068 Positive Predictive Value RNAshapes: 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	44 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAfold: 0.603 Sensitivity MXScarna(seed): 0.562 RNAfold: 0.548 Positive Predictive Value MXScarna(seed): 0.809 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.577 RNAfold: 0.519 Sensitivity CentroidFold: 0.493 RNAfold: 0.475 Positive Predictive Value CentroidFold: 0.676 RNAfold: 0.568 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAfold: 0.566 Sensitivity CentroidAlifold(20): 0.520 RNAfold: 0.505 Positive Predictive Value CentroidAlifold(20): 0.892 RNAfold: 0.638 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAfold: 0.567 Sensitivity RNAalifold(20): 0.491 RNAfold: 0.503 Positive Predictive Value RNAalifold(20): 0.849 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.634 RNAfold: 0.567 Sensitivity RNASampler(20): 0.477 RNAfold: 0.503 Positive Predictive Value RNASampler(20): 0.844 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	121 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.527 RNAfold: 0.504 Sensitivity Sfold: 0.448 RNAfold: 0.454 Positive Predictive Value Sfold: 0.621 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.628 RNAfold: 0.567 Sensitivity MXScarna(20): 0.523 RNAfold: 0.503 Positive Predictive Value MXScarna(20): 0.757 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	121 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.575 RNAfold: 0.504 Sensitivity Contrafold: 0.511 RNAfold: 0.454 Positive Predictive Value Contrafold: 0.648 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.679 RNAfold: 0.662 Sensitivity Fold: 0.618 RNAfold: 0.604 Positive Predictive Value Fold: 0.751 RNAfold: 0.729 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	118 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.662 RNAfold: 0.651 Sensitivity HotKnots: 0.600 RNAfold: 0.587 Positive Predictive Value HotKnots: 0.736 RNAfold: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAfold: 0.635 Sensitivity CentroidHomfold‑LAST: 0.515 RNAfold: 0.562 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAfold: 0.724 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.675 RNAfold: 0.628 Sensitivity IPknot: 0.573 RNAfold: 0.556 Positive Predictive Value IPknot: 0.801 RNAfold: 0.717 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.617 RNAfold: 0.571 Sensitivity MaxExpect: 0.540 RNAfold: 0.507 Positive Predictive Value MaxExpect: 0.705 RNAfold: 0.642 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08	121 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.508 RNAfold: 0.504 Sensitivity UNAFold: 0.454 RNAfold: 0.454 Positive Predictive Value UNAFold: 0.569 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 5.62644058675e-08	30 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.705 RNAfold: 0.624 Sensitivity ContextFold: 0.594 RNAfold: 0.554 Positive Predictive Value ContextFold: 0.843 RNAfold: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.651 RNAshapes: 0.650 Sensitivity RNAfold: 0.587 RNAshapes: 0.580 Positive Predictive Value RNAfold: 0.726 RNAshapes: 0.733 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.27038065226		+ RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.504 PknotsRG: 0.495 Sensitivity RNAfold: 0.454 PknotsRG: 0.447 Positive Predictive Value RNAfold: 0.559 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAfold: 0.600 Sensitivity CentroidAlifold(seed): 0.419 RNAfold: 0.545 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAfold: 0.664 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.0853441262641	+ RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.651 ProbKnot: 0.646 Sensitivity RNAfold: 0.593 ProbKnot: 0.597 Positive Predictive Value RNAfold: 0.718 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 6.06606238843e-08	- Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.582 RNAfold: 0.567 Sensitivity Murlet(20): 0.423 RNAfold: 0.503 Positive Predictive Value Murlet(20): 0.804 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.96741624608e-07	- Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.582 RNAfold: 0.567 Sensitivity Carnac(20): 0.371 RNAfold: 0.503 Positive Predictive Value Carnac(20): 0.915 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.29540574715e-07	= Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.491 RNAfold: 0.488 Sensitivity Afold: 0.446 RNAfold: 0.443 Positive Predictive Value Afold: 0.541 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 0.00324372766907	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.651 RNAsubopt: 0.635 Sensitivity RNAfold: 0.587 RNAsubopt: 0.574 Positive Predictive Value RNAfold: 0.726 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.672 Cylofold: 0.648 Sensitivity RNAfold: 0.603 Cylofold: 0.559 Positive Predictive Value RNAfold: 0.756 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.503 McQFold: 0.443 Sensitivity RNAfold: 0.453 McQFold: 0.348 Positive Predictive Value RNAfold: 0.558 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.620 RNAalifold(seed): 0.593 Sensitivity RNAfold: 0.568 RNAalifold(seed): 0.397 Positive Predictive Value RNAfold: 0.680 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.674 Pknots: 0.634 Sensitivity RNAfold: 0.602 Pknots: 0.575 Positive Predictive Value RNAfold: 0.760 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-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 RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.712 RNASampler(seed): 0.673 Sensitivity RNAfold: 0.659 RNASampler(seed): 0.535 Positive Predictive Value RNAfold: 0.773 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.00627773251e-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: 5.6410608252e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.570 RSpredict(20): 0.547 Sensitivity RNAfold: 0.509 RSpredict(20): 0.428 Positive Predictive Value RNAfold: 0.643 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 7.27211512036e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.567 Mastr(20): 0.525 Sensitivity RNAfold: 0.503 Mastr(20): 0.346 Positive Predictive Value RNAfold: 0.644 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.651 Vsfold4: 0.562 Sensitivity RNAfold: 0.587 Vsfold4: 0.481 Positive Predictive Value RNAfold: 0.726 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.624 RNASLOpt: 0.591 Sensitivity RNAfold: 0.554 RNASLOpt: 0.498 Positive Predictive Value RNAfold: 0.709 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.556 Multilign(20): 0.521 Sensitivity RNAfold: 0.482 Multilign(20): 0.428 Positive Predictive Value RNAfold: 0.648 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.628 RNAwolf: 0.512 Sensitivity RNAfold: 0.556 RNAwolf: 0.479 Positive Predictive Value RNAfold: 0.717 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.678 Murlet(seed): 0.539 Sensitivity RNAfold: 0.604 Murlet(seed): 0.337 Positive Predictive Value RNAfold: 0.765 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.691 MCFold: 0.577 Sensitivity RNAfold: 0.623 MCFold: 0.597 Positive Predictive Value RNAfold: 0.772 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.650 Vsfold5: 0.528 Sensitivity RNAfold: 0.586 Vsfold5: 0.458 Positive Predictive Value RNAfold: 0.726 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.707 RDfolder: 0.596 Sensitivity RNAfold: 0.631 RDfolder: 0.495 Positive Predictive Value RNAfold: 0.799 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.603 RSpredict(seed): 0.314 Sensitivity RNAfold: 0.548 RSpredict(seed): 0.161 Positive Predictive Value RNAfold: 0.667 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.565 PPfold(seed): 0.102 Sensitivity RNAfold: 0.476 PPfold(seed): 0.020 Positive Predictive Value RNAfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.40919803867e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.639 NanoFolder: 0.490 Sensitivity RNAfold: 0.567 NanoFolder: 0.495 Positive Predictive Value RNAfold: 0.728 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.600 Mastr(seed): 0.258 Sensitivity RNAfold: 0.542 Mastr(seed): 0.075 Positive Predictive Value RNAfold: 0.667 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.672 Multilign(seed): 0.593 Sensitivity RNAfold: 0.563 Multilign(seed): 0.475 Positive Predictive Value RNAfold: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAfold: 0.515 Sensitivity PETfold_pre2.0(seed): 0.551 RNAfold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.620 RNAfold: 0.587 Sensitivity TurboFold(20): 0.500 RNAfold: 0.507 Positive Predictive Value TurboFold(20): 0.775 RNAfold: 0.687 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAfold: 0.476 Sensitivity PETfold_pre2.0(20): 0.497 RNAfold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.578 TurboFold(seed): 0.550 Sensitivity RNAfold: 0.502 TurboFold(seed): 0.456 Positive Predictive Value RNAfold: 0.673 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.663 RNAfold: 0.587 Sensitivity PPfold(20): 0.514 RNAfold: 0.507 Positive Predictive Value PPfold(20): 0.861 RNAfold: 0.687 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.667 Carnac(seed): 0.260 Sensitivity RNAfold: 0.599 Carnac(seed): 0.068 Positive Predictive Value RNAfold: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	44 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.673 PknotsRG: 0.602 Sensitivity MXScarna(seed): 0.562 PknotsRG: 0.549 Positive Predictive Value MXScarna(seed): 0.809 PknotsRG: 0.665 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.577 PknotsRG: 0.510 Sensitivity CentroidFold: 0.493 PknotsRG: 0.468 Positive Predictive Value CentroidFold: 0.676 PknotsRG: 0.558 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.680 PknotsRG: 0.576 Sensitivity CentroidAlifold(20): 0.520 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(20): 0.892 PknotsRG: 0.647 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.644 PknotsRG: 0.579 Sensitivity RNAalifold(20): 0.491 PknotsRG: 0.516 Positive Predictive Value RNAalifold(20): 0.849 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.634 PknotsRG: 0.579 Sensitivity RNASampler(20): 0.477 PknotsRG: 0.516 Positive Predictive Value RNASampler(20): 0.844 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	121 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.527 PknotsRG: 0.495 Sensitivity Sfold: 0.448 PknotsRG: 0.447 Positive Predictive Value Sfold: 0.621 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.628 PknotsRG: 0.579 Sensitivity MXScarna(20): 0.523 PknotsRG: 0.516 Positive Predictive Value MXScarna(20): 0.757 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.575 PknotsRG: 0.495 Sensitivity Contrafold: 0.511 PknotsRG: 0.447 Positive Predictive Value Contrafold: 0.648 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.679 PknotsRG: 0.659 Sensitivity Fold: 0.618 PknotsRG: 0.604 Positive Predictive Value Fold: 0.751 PknotsRG: 0.722 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	118 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.662 PknotsRG: 0.646 Sensitivity HotKnots: 0.600 PknotsRG: 0.585 Positive Predictive Value HotKnots: 0.736 PknotsRG: 0.718 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 PknotsRG: 0.641 Sensitivity CentroidHomfold‑LAST: 0.515 PknotsRG: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.873 PknotsRG: 0.723 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.675 PknotsRG: 0.637 Sensitivity IPknot: 0.573 PknotsRG: 0.572 Positive Predictive Value IPknot: 0.801 PknotsRG: 0.716 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.617 PknotsRG: 0.559 Sensitivity MaxExpect: 0.540 PknotsRG: 0.499 Positive Predictive Value MaxExpect: 0.705 PknotsRG: 0.628 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.508 PknotsRG: 0.495 Sensitivity UNAFold: 0.454 PknotsRG: 0.447 Positive Predictive Value UNAFold: 0.569 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.705 PknotsRG: 0.637 Sensitivity ContextFold: 0.594 PknotsRG: 0.574 Positive Predictive Value ContextFold: 0.843 PknotsRG: 0.713 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs PknotsRG Matthews Correlation Coefficient RNAshapes: 0.650 PknotsRG: 0.646 Sensitivity RNAshapes: 0.580 PknotsRG: 0.585 Positive Predictive Value RNAshapes: 0.733 PknotsRG: 0.718 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 2.91197157422e-05	121 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.504 PknotsRG: 0.495 Sensitivity RNAfold: 0.454 PknotsRG: 0.447 Positive Predictive Value RNAfold: 0.559 PknotsRG: 0.548 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08		= CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 PknotsRG: 0.600 Sensitivity CentroidAlifold(seed): 0.419 PknotsRG: 0.547 Positive Predictive Value CentroidAlifold(seed): 0.878 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.125446474224	+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.652 ProbKnot: 0.646 Sensitivity PknotsRG: 0.597 ProbKnot: 0.597 Positive Predictive Value PknotsRG: 0.715 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 5.21776328505e-08	= Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.582 PknotsRG: 0.579 Sensitivity Murlet(20): 0.423 PknotsRG: 0.516 Positive Predictive Value Murlet(20): 0.804 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0196173936984	= Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.582 PknotsRG: 0.579 Sensitivity Carnac(20): 0.371 PknotsRG: 0.516 Positive Predictive Value Carnac(20): 0.915 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00230851584557	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.491 PknotsRG: 0.477 Sensitivity Afold: 0.446 PknotsRG: 0.434 Positive Predictive Value Afold: 0.541 PknotsRG: 0.526 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.646 RNAsubopt: 0.635 Sensitivity PknotsRG: 0.585 RNAsubopt: 0.574 Positive Predictive Value PknotsRG: 0.718 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.675 Cylofold: 0.648 Sensitivity PknotsRG: 0.609 Cylofold: 0.559 Positive Predictive Value PknotsRG: 0.754 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.494 McQFold: 0.443 Sensitivity PknotsRG: 0.446 McQFold: 0.348 Positive Predictive Value PknotsRG: 0.547 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.621 RNAalifold(seed): 0.593 Sensitivity PknotsRG: 0.571 RNAalifold(seed): 0.397 Positive Predictive Value PknotsRG: 0.678 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.668 Pknots: 0.634 Sensitivity PknotsRG: 0.600 Pknots: 0.575 Positive Predictive Value PknotsRG: 0.751 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ 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 RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.687 RNASampler(seed): 0.673 Sensitivity PknotsRG: 0.637 RNASampler(seed): 0.535 Positive Predictive Value PknotsRG: 0.745 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.20802062638e-07	+ 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: 3.85233844192e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.581 RSpredict(20): 0.547 Sensitivity PknotsRG: 0.521 RSpredict(20): 0.428 Positive Predictive Value PknotsRG: 0.651 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.579 Mastr(20): 0.525 Sensitivity PknotsRG: 0.516 Mastr(20): 0.346 Positive Predictive Value PknotsRG: 0.653 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.646 Vsfold4: 0.562 Sensitivity PknotsRG: 0.585 Vsfold4: 0.481 Positive Predictive Value PknotsRG: 0.718 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.637 RNASLOpt: 0.591 Sensitivity PknotsRG: 0.574 RNASLOpt: 0.498 Positive Predictive Value PknotsRG: 0.713 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.592 Multilign(20): 0.521 Sensitivity PknotsRG: 0.521 Multilign(20): 0.428 Positive Predictive Value PknotsRG: 0.678 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.637 RNAwolf: 0.512 Sensitivity PknotsRG: 0.572 RNAwolf: 0.479 Positive Predictive Value PknotsRG: 0.716 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.679 Murlet(seed): 0.539 Sensitivity PknotsRG: 0.609 Murlet(seed): 0.337 Positive Predictive Value PknotsRG: 0.762 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.685 MCFold: 0.577 Sensitivity PknotsRG: 0.620 MCFold: 0.597 Positive Predictive Value PknotsRG: 0.763 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.645 Vsfold5: 0.528 Sensitivity PknotsRG: 0.584 Vsfold5: 0.458 Positive Predictive Value PknotsRG: 0.718 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.704 RDfolder: 0.596 Sensitivity PknotsRG: 0.631 RDfolder: 0.495 Positive Predictive Value PknotsRG: 0.795 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.602 RSpredict(seed): 0.314 Sensitivity PknotsRG: 0.549 RSpredict(seed): 0.161 Positive Predictive Value PknotsRG: 0.665 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.600 PPfold(seed): 0.102 Sensitivity PknotsRG: 0.513 PPfold(seed): 0.020 Positive Predictive Value PknotsRG: 0.709 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.642 NanoFolder: 0.490 Sensitivity PknotsRG: 0.574 NanoFolder: 0.495 Positive Predictive Value PknotsRG: 0.724 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.600 Mastr(seed): 0.258 Sensitivity PknotsRG: 0.545 Mastr(seed): 0.075 Positive Predictive Value PknotsRG: 0.666 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.667 Multilign(seed): 0.593 Sensitivity PknotsRG: 0.557 Multilign(seed): 0.475 Positive Predictive Value PknotsRG: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PknotsRG: 0.569 Sensitivity PETfold_pre2.0(seed): 0.551 PknotsRG: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.628 TurboFold(20): 0.620 Sensitivity PknotsRG: 0.552 TurboFold(20): 0.500 Positive Predictive Value PknotsRG: 0.721 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(20): 0.497 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 PknotsRG: 0.618 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.621 TurboFold(seed): 0.550 Sensitivity PknotsRG: 0.548 TurboFold(seed): 0.456 Positive Predictive Value PknotsRG: 0.711 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.663 PknotsRG: 0.628 Sensitivity PPfold(20): 0.514 PknotsRG: 0.552 Positive Predictive Value PPfold(20): 0.861 PknotsRG: 0.721 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.668 Carnac(seed): 0.260 Sensitivity PknotsRG: 0.604 Carnac(seed): 0.068 Positive Predictive Value PknotsRG: 0.745 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	43 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.671 CentroidAlifold(seed): 0.605 Sensitivity MXScarna(seed): 0.560 CentroidAlifold(seed): 0.419 Positive Predictive Value MXScarna(seed): 0.807 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.625 CentroidAlifold(seed): 0.605 Sensitivity CentroidFold: 0.545 CentroidAlifold(seed): 0.419 Positive Predictive Value CentroidFold: 0.719 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 CentroidAlifold(seed): 0.629 Sensitivity CentroidAlifold(20): 0.520 CentroidAlifold(seed): 0.430 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 CentroidAlifold(seed): 0.629 Sensitivity RNAalifold(20): 0.492 CentroidAlifold(seed): 0.430 Positive Predictive Value RNAalifold(20): 0.842 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.87980998248e-07	26 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.636 CentroidAlifold(seed): 0.629 Sensitivity RNASampler(20): 0.484 CentroidAlifold(seed): 0.430 Positive Predictive Value RNASampler(20): 0.840 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.00322321493779	43 Sfold vs CentroidAlifold(seed) Matthews Correlation Coefficient Sfold: 0.605 CentroidAlifold(seed): 0.605 Sensitivity Sfold: 0.523 CentroidAlifold(seed): 0.419 Positive Predictive Value Sfold: 0.705 CentroidAlifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.333157548069	26 MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.630 CentroidAlifold(seed): 0.629 Sensitivity MXScarna(20): 0.526 CentroidAlifold(seed): 0.430 Positive Predictive Value MXScarna(20): 0.758 CentroidAlifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0920574641616	43 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Contrafold: 0.596 Sensitivity CentroidAlifold(seed): 0.419 Contrafold: 0.541 Positive Predictive Value CentroidAlifold(seed): 0.878 Contrafold: 0.661 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.00517730549486	31 Fold vs CentroidAlifold(seed) Matthews Correlation Coefficient Fold: 0.625 CentroidAlifold(seed): 0.609 Sensitivity Fold: 0.569 CentroidAlifold(seed): 0.424 Positive Predictive Value Fold: 0.690 CentroidAlifold(seed): 0.877 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.76761760679e-06	43 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 HotKnots: 0.599 Sensitivity CentroidAlifold(seed): 0.419 HotKnots: 0.547 Positive Predictive Value CentroidAlifold(seed): 0.878 HotKnots: 0.660 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.000451186043411	12 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 CentroidAlifold(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.501 CentroidAlifold(seed): 0.355 Positive Predictive Value CentroidHomfold‑LAST: 0.808 CentroidAlifold(seed): 0.937 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.47941000302e-08	11 IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.590 CentroidAlifold(seed): 0.583 Sensitivity IPknot: 0.471 CentroidAlifold(seed): 0.347 Positive Predictive Value IPknot: 0.747 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00654707608169	40 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.608 MaxExpect: 0.605 Sensitivity CentroidAlifold(seed): 0.422 MaxExpect: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.877 MaxExpect: 0.677 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.0024921586113	43 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 UNAFold: 0.596 Sensitivity CentroidAlifold(seed): 0.419 UNAFold: 0.537 Positive Predictive Value CentroidAlifold(seed): 0.878 UNAFold: 0.665 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 1.59851305843e-05	8 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.616 CentroidAlifold(seed): 0.542 Sensitivity ContextFold: 0.476 CentroidAlifold(seed): 0.299 Positive Predictive Value ContextFold: 0.801 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	43 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAshapes: 0.595 Sensitivity CentroidAlifold(seed): 0.419 RNAshapes: 0.535 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAshapes: 0.665 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 2.71856013146e-06	43 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAfold: 0.600 Sensitivity CentroidAlifold(seed): 0.419 RNAfold: 0.545 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAfold: 0.664 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.0853441262641	43 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 PknotsRG: 0.600 Sensitivity CentroidAlifold(seed): 0.419 PknotsRG: 0.547 Positive Predictive Value CentroidAlifold(seed): 0.878 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.125446474224		+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.613 ProbKnot: 0.570 Sensitivity CentroidAlifold(seed): 0.418 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.904 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Murlet(20): 0.581 Sensitivity CentroidAlifold(seed): 0.430 Murlet(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.923 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Carnac(20): 0.584 Sensitivity CentroidAlifold(seed): 0.430 Carnac(20): 0.375 Positive Predictive Value CentroidAlifold(seed): 0.923 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.601 Afold: 0.566 Sensitivity CentroidAlifold(seed): 0.424 Afold: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.854 Afold: 0.608 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAsubopt: 0.567 Sensitivity CentroidAlifold(seed): 0.419 RNAsubopt: 0.519 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAsubopt: 0.624 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.640 CentroidAlifold(seed): 0.638 Sensitivity Cylofold: 0.553 CentroidAlifold(seed): 0.437 Positive Predictive Value Cylofold: 0.747 CentroidAlifold(seed): 0.936 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.0974231606503	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 McQFold: 0.562 Sensitivity CentroidAlifold(seed): 0.419 McQFold: 0.497 Positive Predictive Value CentroidAlifold(seed): 0.878 McQFold: 0.640 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.660 RNAalifold(seed): 0.593 Sensitivity CentroidAlifold(seed): 0.504 RNAalifold(seed): 0.399 Positive Predictive Value CentroidAlifold(seed): 0.866 RNAalifold(seed): 0.886 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	= CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.614 Pknots: 0.612 Sensitivity CentroidAlifold(seed): 0.424 Pknots: 0.559 Positive Predictive Value CentroidAlifold(seed): 0.894 Pknots: 0.676 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.226387597291	- 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: 5.10776592382e-08	= CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.668 RNASampler(seed): 0.665 Sensitivity CentroidAlifold(seed): 0.532 RNASampler(seed): 0.525 Positive Predictive Value CentroidAlifold(seed): 0.844 RNASampler(seed): 0.846 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.673410491699	? 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 RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 RSpredict(20): 0.543 Sensitivity CentroidAlifold(seed): 0.430 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.923 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Mastr(20): 0.521 Sensitivity CentroidAlifold(seed): 0.430 Mastr(20): 0.342 Positive Predictive Value CentroidAlifold(seed): 0.923 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Vsfold4: 0.513 Sensitivity CentroidAlifold(seed): 0.419 Vsfold4: 0.441 Positive Predictive Value CentroidAlifold(seed): 0.878 Vsfold4: 0.601 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.542 RNASLOpt: 0.474 Sensitivity CentroidAlifold(seed): 0.299 RNASLOpt: 0.374 Positive Predictive Value CentroidAlifold(seed): 0.987 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.645 Multilign(20): 0.521 Sensitivity CentroidAlifold(seed): 0.449 Multilign(20): 0.428 Positive Predictive Value CentroidAlifold(seed): 0.931 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.35568223474e-09	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 RNAwolf: 0.414 Sensitivity CentroidAlifold(seed): 0.347 RNAwolf: 0.375 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.08932646657e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 Murlet(seed): 0.540 Sensitivity CentroidAlifold(seed): 0.549 Murlet(seed): 0.338 Positive Predictive Value CentroidAlifold(seed): 0.883 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 MCFold: 0.498 Sensitivity CentroidAlifold(seed): 0.433 MCFold: 0.522 Positive Predictive Value CentroidAlifold(seed): 0.893 MCFold: 0.483 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Vsfold5: 0.487 Sensitivity CentroidAlifold(seed): 0.419 Vsfold5: 0.423 Positive Predictive Value CentroidAlifold(seed): 0.878 Vsfold5: 0.566 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.611 RDfolder: 0.550 Sensitivity CentroidAlifold(seed): 0.435 RDfolder: 0.456 Positive Predictive Value CentroidAlifold(seed): 0.866 RDfolder: 0.672 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RSpredict(seed): 0.308 Sensitivity CentroidAlifold(seed): 0.419 RSpredict(seed): 0.156 Positive Predictive Value CentroidAlifold(seed): 0.878 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 PPfold(seed): 0.102 Sensitivity CentroidAlifold(seed): 0.347 PPfold(seed): 0.020 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.00627773251e-08	? CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.533 NanoFolder: 0.346 Sensitivity CentroidAlifold(seed): 0.289 NanoFolder: 0.353 Positive Predictive Value CentroidAlifold(seed): 0.986 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Mastr(seed): 0.264 Sensitivity CentroidAlifold(seed): 0.419 Mastr(seed): 0.078 Positive Predictive Value CentroidAlifold(seed): 0.878 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 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	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.657 Multilign(seed): 0.593 Sensitivity CentroidAlifold(seed): 0.481 Multilign(seed): 0.475 Positive Predictive Value CentroidAlifold(seed): 0.905 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidAlifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidAlifold(seed): 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 TurboFold(20): 0.620 Sensitivity CentroidAlifold(seed): 0.421 TurboFold(20): 0.500 Positive Predictive Value CentroidAlifold(seed): 0.931 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidAlifold(seed): 0.613 Sensitivity PETfold_pre2.0(20): 0.497 CentroidAlifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.615 TurboFold(seed): 0.550 Sensitivity CentroidAlifold(seed): 0.410 TurboFold(seed): 0.456 Positive Predictive Value CentroidAlifold(seed): 0.928 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 CentroidAlifold(seed): 0.624 Sensitivity PPfold(20): 0.514 CentroidAlifold(seed): 0.421 Positive Predictive Value PPfold(20): 0.861 CentroidAlifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.674 Carnac(seed): 0.240 Sensitivity CentroidAlifold(seed): 0.511 Carnac(seed): 0.058 Positive Predictive Value CentroidAlifold(seed): 0.893 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	26 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.653 ProbKnot: 0.570 Sensitivity MXScarna(seed): 0.541 ProbKnot: 0.529 Positive Predictive Value MXScarna(seed): 0.791 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	74 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.674 ProbKnot: 0.646 Sensitivity CentroidFold: 0.590 ProbKnot: 0.597 Positive Predictive Value CentroidFold: 0.774 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.671 ProbKnot: 0.586 Sensitivity CentroidAlifold(20): 0.500 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(20): 0.904 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	18 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.626 ProbKnot: 0.586 Sensitivity RNAalifold(20): 0.468 ProbKnot: 0.529 Positive Predictive Value RNAalifold(20): 0.841 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	18 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.625 ProbKnot: 0.586 Sensitivity RNASampler(20): 0.460 ProbKnot: 0.529 Positive Predictive Value RNASampler(20): 0.851 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	74 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.667 ProbKnot: 0.646 Sensitivity Sfold: 0.583 ProbKnot: 0.597 Positive Predictive Value Sfold: 0.766 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.628 ProbKnot: 0.586 Sensitivity MXScarna(20): 0.520 ProbKnot: 0.529 Positive Predictive Value MXScarna(20): 0.762 ProbKnot: 0.653 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.54229534325e-08	74 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.659 ProbKnot: 0.646 Sensitivity Contrafold: 0.597 ProbKnot: 0.597 Positive Predictive Value Contrafold: 0.732 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 Fold vs ProbKnot Matthews Correlation Coefficient Fold: 0.660 ProbKnot: 0.646 Sensitivity Fold: 0.600 ProbKnot: 0.597 Positive Predictive Value Fold: 0.730 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 6.06606238843e-08	74 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.659 ProbKnot: 0.646 Sensitivity HotKnots: 0.604 ProbKnot: 0.597 Positive Predictive Value HotKnots: 0.722 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 ProbKnot: 0.612 Sensitivity CentroidHomfold‑LAST: 0.515 ProbKnot: 0.556 Positive Predictive Value CentroidHomfold‑LAST: 0.873 ProbKnot: 0.680 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.675 ProbKnot: 0.610 Sensitivity IPknot: 0.573 ProbKnot: 0.555 Positive Predictive Value IPknot: 0.801 ProbKnot: 0.679 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.653 ProbKnot: 0.646 Sensitivity MaxExpect: 0.590 ProbKnot: 0.597 Positive Predictive Value MaxExpect: 0.728 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.650 ProbKnot: 0.646 Sensitivity UNAFold: 0.589 ProbKnot: 0.597 Positive Predictive Value UNAFold: 0.721 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.5875416339e-07	30 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.705 ProbKnot: 0.611 Sensitivity ContextFold: 0.594 ProbKnot: 0.558 Positive Predictive Value ContextFold: 0.843 ProbKnot: 0.676 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	74 RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.653 ProbKnot: 0.646 Sensitivity RNAshapes: 0.589 ProbKnot: 0.597 Positive Predictive Value RNAshapes: 0.728 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.000114481332584	74 RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.651 ProbKnot: 0.646 Sensitivity RNAfold: 0.593 ProbKnot: 0.597 Positive Predictive Value RNAfold: 0.718 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 6.06606238843e-08	74 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.652 ProbKnot: 0.646 Sensitivity PknotsRG: 0.597 ProbKnot: 0.597 Positive Predictive Value PknotsRG: 0.715 ProbKnot: 0.703 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 5.21776328505e-08	26 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.613 ProbKnot: 0.570 Sensitivity CentroidAlifold(seed): 0.418 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.904 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.586 Murlet(20): 0.575 Sensitivity ProbKnot: 0.529 Murlet(20): 0.413 Positive Predictive Value ProbKnot: 0.653 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 5.00648371734e-07	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.586 Carnac(20): 0.558 Sensitivity ProbKnot: 0.529 Carnac(20): 0.339 Positive Predictive Value ProbKnot: 0.653 Carnac(20): 0.924 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.652 Afold: 0.647 Sensitivity ProbKnot: 0.612 Afold: 0.605 Positive Predictive Value ProbKnot: 0.699 Afold: 0.695 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 0.000186465496926	= ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.646 RNAsubopt: 0.644 Sensitivity ProbKnot: 0.597 RNAsubopt: 0.587 Positive Predictive Value ProbKnot: 0.703 RNAsubopt: 0.712 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.0782705756228	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.679 Cylofold: 0.644 Sensitivity ProbKnot: 0.621 Cylofold: 0.555 Positive Predictive Value ProbKnot: 0.748 Cylofold: 0.755 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.643 McQFold: 0.633 Sensitivity ProbKnot: 0.595 McQFold: 0.561 Positive Predictive Value ProbKnot: 0.700 McQFold: 0.719 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.37177523642e-07	= ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.520 RNAalifold(seed): 0.519 Sensitivity ProbKnot: 0.487 RNAalifold(seed): 0.320 Positive Predictive Value ProbKnot: 0.559 RNAalifold(seed): 0.843 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.486848903635	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.680 Pknots: 0.649 Sensitivity ProbKnot: 0.625 Pknots: 0.589 Positive Predictive Value ProbKnot: 0.745 Pknots: 0.722 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-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	? RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.568 ProbKnot: 0.543 Sensitivity RNASampler(seed): 0.429 ProbKnot: 0.528 Positive Predictive Value RNASampler(seed): 0.758 ProbKnot: 0.564 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- 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: 0.000120940900885	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.586 RSpredict(20): 0.524 Sensitivity ProbKnot: 0.529 RSpredict(20): 0.403 Positive Predictive Value ProbKnot: 0.653 RSpredict(20): 0.684 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.586 Mastr(20): 0.491 Sensitivity ProbKnot: 0.529 Mastr(20): 0.300 Positive Predictive Value ProbKnot: 0.653 Mastr(20): 0.808 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.646 Vsfold4: 0.547 Sensitivity ProbKnot: 0.597 Vsfold4: 0.471 Positive Predictive Value ProbKnot: 0.703 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.611 RNASLOpt: 0.591 Sensitivity ProbKnot: 0.558 RNASLOpt: 0.498 Positive Predictive Value ProbKnot: 0.676 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.25365426827e-07	+ ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.533 Multilign(20): 0.521 Sensitivity ProbKnot: 0.479 Multilign(20): 0.428 Positive Predictive Value ProbKnot: 0.600 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.4327622078e-07	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.610 RNAwolf: 0.512 Sensitivity ProbKnot: 0.555 RNAwolf: 0.479 Positive Predictive Value ProbKnot: 0.679 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.557 Murlet(seed): 0.499 Sensitivity ProbKnot: 0.513 Murlet(seed): 0.292 Positive Predictive Value ProbKnot: 0.611 Murlet(seed): 0.857 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.682 MCFold: 0.589 Sensitivity ProbKnot: 0.632 MCFold: 0.610 Positive Predictive Value ProbKnot: 0.741 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.645 Vsfold5: 0.516 Sensitivity ProbKnot: 0.596 Vsfold5: 0.451 Positive Predictive Value ProbKnot: 0.701 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.710 RDfolder: 0.609 Sensitivity ProbKnot: 0.657 RDfolder: 0.514 Positive Predictive Value ProbKnot: 0.776 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.570 RSpredict(seed): 0.228 Sensitivity ProbKnot: 0.529 RSpredict(seed): 0.106 Positive Predictive Value ProbKnot: 0.618 RSpredict(seed): 0.498 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.513 PPfold(seed): 0.102 Sensitivity ProbKnot: 0.457 PPfold(seed): 0.020 Positive Predictive Value ProbKnot: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.84361416392e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.606 NanoFolder: 0.490 Sensitivity ProbKnot: 0.552 NanoFolder: 0.495 Positive Predictive Value ProbKnot: 0.673 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.48104284388e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.570 Mastr(seed): 0.213 Sensitivity ProbKnot: 0.529 Mastr(seed): 0.046 Positive Predictive Value ProbKnot: 0.618 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-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	? Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.593 ProbKnot: 0.562 Sensitivity Multilign(seed): 0.475 ProbKnot: 0.481 Positive Predictive Value Multilign(seed): 0.750 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ProbKnot: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 ProbKnot: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.620 ProbKnot: 0.574 Sensitivity TurboFold(20): 0.500 ProbKnot: 0.514 Positive Predictive Value TurboFold(20): 0.775 ProbKnot: 0.648 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ProbKnot: 0.488 Sensitivity PETfold_pre2.0(20): 0.497 ProbKnot: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ProbKnot: 0.544 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.550 ProbKnot: 0.526 Sensitivity TurboFold(seed): 0.456 ProbKnot: 0.470 Positive Predictive Value TurboFold(seed): 0.672 ProbKnot: 0.596 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.663 ProbKnot: 0.574 Sensitivity PPfold(20): 0.514 ProbKnot: 0.514 Positive Predictive Value PPfold(20): 0.861 ProbKnot: 0.648 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.596 Carnac(seed): 0.189 Sensitivity ProbKnot: 0.545 Carnac(seed): 0.036 Positive Predictive Value ProbKnot: 0.658 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08
Murlet(20)	27 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Murlet(20): 0.582 Sensitivity MXScarna(seed): 0.556 Murlet(20): 0.425 Positive Predictive Value MXScarna(seed): 0.805 Murlet(20): 0.800 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.597 Murlet(20): 0.581 Sensitivity CentroidFold: 0.506 Murlet(20): 0.425 Positive Predictive Value CentroidFold: 0.707 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.18973841657e-07	26 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Murlet(20): 0.581 Sensitivity CentroidAlifold(20): 0.520 Murlet(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.892 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Murlet(20): 0.582 Sensitivity RNAalifold(20): 0.491 Murlet(20): 0.423 Positive Predictive Value RNAalifold(20): 0.849 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Murlet(20): 0.582 Sensitivity RNASampler(20): 0.477 Murlet(20): 0.423 Positive Predictive Value RNASampler(20): 0.844 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.590 Murlet(20): 0.582 Sensitivity Sfold: 0.493 Murlet(20): 0.423 Positive Predictive Value Sfold: 0.709 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.13258597535e-06	28 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Murlet(20): 0.582 Sensitivity MXScarna(20): 0.523 Murlet(20): 0.423 Positive Predictive Value MXScarna(20): 0.757 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.582 Contrafold: 0.544 Sensitivity Murlet(20): 0.423 Contrafold: 0.481 Positive Predictive Value Murlet(20): 0.804 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.610 Murlet(20): 0.575 Sensitivity Fold: 0.542 Murlet(20): 0.413 Positive Predictive Value Fold: 0.689 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.82974185391e-08	28 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.582 HotKnots: 0.577 Sensitivity Murlet(20): 0.423 HotKnots: 0.514 Positive Predictive Value Murlet(20): 0.804 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0546456716999	9 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Murlet(20): 0.576 Sensitivity CentroidHomfold‑LAST: 0.524 Murlet(20): 0.438 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.581 IPknot: 0.571 Sensitivity Murlet(20): 0.433 IPknot: 0.463 Positive Predictive Value Murlet(20): 0.785 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.588 Murlet(20): 0.581 Sensitivity MaxExpect: 0.516 Murlet(20): 0.425 Positive Predictive Value MaxExpect: 0.675 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 9.71546425945e-06	28 UNAFold vs Murlet(20) Matthews Correlation Coefficient UNAFold: 0.585 Murlet(20): 0.582 Sensitivity UNAFold: 0.512 Murlet(20): 0.423 Positive Predictive Value UNAFold: 0.672 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0414928403863	5 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.579 Murlet(20): 0.496 Sensitivity ContextFold: 0.443 Murlet(20): 0.353 Positive Predictive Value ContextFold: 0.763 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.582 RNAshapes: 0.577 Sensitivity Murlet(20): 0.423 RNAshapes: 0.506 Positive Predictive Value Murlet(20): 0.804 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0440733078056	28 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.582 RNAfold: 0.567 Sensitivity Murlet(20): 0.423 RNAfold: 0.503 Positive Predictive Value Murlet(20): 0.804 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.96741624608e-07	28 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.582 PknotsRG: 0.579 Sensitivity Murlet(20): 0.423 PknotsRG: 0.516 Positive Predictive Value Murlet(20): 0.804 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0196173936984	26 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Murlet(20): 0.581 Sensitivity CentroidAlifold(seed): 0.430 Murlet(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.923 Murlet(20): 0.798 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.586 Murlet(20): 0.575 Sensitivity ProbKnot: 0.529 Murlet(20): 0.413 Positive Predictive Value ProbKnot: 0.653 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 5.00648371734e-07		= Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.582 Carnac(20): 0.582 Sensitivity Murlet(20): 0.423 Carnac(20): 0.371 Positive Predictive Value Murlet(20): 0.804 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.379481211626	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.541 Afold: 0.518 Sensitivity Murlet(20): 0.391 Afold: 0.469 Positive Predictive Value Murlet(20): 0.753 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.45559089896e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.582 RNAsubopt: 0.550 Sensitivity Murlet(20): 0.423 RNAsubopt: 0.492 Positive Predictive Value Murlet(20): 0.804 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.649 Cylofold: 0.608 Sensitivity Murlet(20): 0.483 Cylofold: 0.523 Positive Predictive Value Murlet(20): 0.878 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.582 McQFold: 0.524 Sensitivity Murlet(20): 0.423 McQFold: 0.454 Positive Predictive Value Murlet(20): 0.804 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	- RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Murlet(20): 0.524 Sensitivity RNAalifold(seed): 0.356 Murlet(20): 0.357 Positive Predictive Value RNAalifold(seed): 0.923 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.57327336088e-08	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.604 Pknots: 0.530 Sensitivity Murlet(20): 0.449 Pknots: 0.483 Positive Predictive Value Murlet(20): 0.818 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ 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: 1.66062906821e-08	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Murlet(20): 0.496 Sensitivity RNASampler(seed): 0.444 Murlet(20): 0.385 Positive Predictive Value RNASampler(seed): 0.768 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.582 RSpredict(20): 0.547 Sensitivity Murlet(20): 0.425 RSpredict(20): 0.428 Positive Predictive Value Murlet(20): 0.800 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.582 Mastr(20): 0.525 Sensitivity Murlet(20): 0.423 Mastr(20): 0.346 Positive Predictive Value Murlet(20): 0.804 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.582 Vsfold4: 0.450 Sensitivity Murlet(20): 0.423 Vsfold4: 0.379 Positive Predictive Value Murlet(20): 0.804 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.496 RNASLOpt: 0.467 Sensitivity Murlet(20): 0.353 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.702 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.557 Multilign(20): 0.521 Sensitivity Murlet(20): 0.404 Multilign(20): 0.428 Positive Predictive Value Murlet(20): 0.775 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.1398907247e-09	? Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.581 RNAwolf: 0.364 Sensitivity Murlet(20): 0.433 RNAwolf: 0.333 Positive Predictive Value Murlet(20): 0.785 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.550 Murlet(seed): 0.491 Sensitivity Murlet(20): 0.384 Murlet(seed): 0.269 Positive Predictive Value Murlet(20): 0.794 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.602 MCFold: 0.421 Sensitivity Murlet(20): 0.454 MCFold: 0.445 Positive Predictive Value Murlet(20): 0.804 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.582 Vsfold5: 0.406 Sensitivity Murlet(20): 0.423 Vsfold5: 0.347 Positive Predictive Value Murlet(20): 0.804 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.651 RDfolder: 0.529 Sensitivity Murlet(20): 0.490 RDfolder: 0.431 Positive Predictive Value Murlet(20): 0.871 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.582 RSpredict(seed): 0.249 Sensitivity Murlet(20): 0.425 RSpredict(seed): 0.110 Positive Predictive Value Murlet(20): 0.800 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.581 PPfold(seed): 0.026 Sensitivity Murlet(20): 0.433 PPfold(seed): 0.004 Positive Predictive Value Murlet(20): 0.785 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.503 NanoFolder: 0.316 Sensitivity Murlet(20): 0.372 NanoFolder: 0.324 Positive Predictive Value Murlet(20): 0.688 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.582 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.423 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.804 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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	? Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Murlet(20): 0.667 Sensitivity Multilign(seed): 0.543 Murlet(20): 0.529 Positive Predictive Value Multilign(seed): 0.852 Murlet(20): 0.849 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.557 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Murlet(20): 0.576 Sensitivity TurboFold(20): 0.500 Murlet(20): 0.438 Positive Predictive Value TurboFold(20): 0.775 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.497 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(20): 0.790 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Murlet(20): 0.554 Sensitivity TurboFold(seed): 0.490 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.729 Murlet(20): 0.747 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.663 Murlet(20): 0.576 Sensitivity PPfold(20): 0.514 Murlet(20): 0.438 Positive Predictive Value PPfold(20): 0.861 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.587 Carnac(seed): 0.197 Sensitivity Murlet(20): 0.425 Carnac(seed): 0.039 Positive Predictive Value Murlet(20): 0.817 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08
Carnac(20)	27 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Carnac(20): 0.586 Sensitivity MXScarna(seed): 0.556 Carnac(20): 0.377 Positive Predictive Value MXScarna(seed): 0.805 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.597 Carnac(20): 0.584 Sensitivity CentroidFold: 0.506 Carnac(20): 0.375 Positive Predictive Value CentroidFold: 0.707 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.80284942886e-07	26 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Carnac(20): 0.584 Sensitivity CentroidAlifold(20): 0.520 Carnac(20): 0.375 Positive Predictive Value CentroidAlifold(20): 0.892 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Carnac(20): 0.582 Sensitivity RNAalifold(20): 0.491 Carnac(20): 0.371 Positive Predictive Value RNAalifold(20): 0.849 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Carnac(20): 0.582 Sensitivity RNASampler(20): 0.477 Carnac(20): 0.371 Positive Predictive Value RNASampler(20): 0.844 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.590 Carnac(20): 0.582 Sensitivity Sfold: 0.493 Carnac(20): 0.371 Positive Predictive Value Sfold: 0.709 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.66995548893e-06	28 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Carnac(20): 0.582 Sensitivity MXScarna(20): 0.523 Carnac(20): 0.371 Positive Predictive Value MXScarna(20): 0.757 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.582 Contrafold: 0.544 Sensitivity Carnac(20): 0.371 Contrafold: 0.481 Positive Predictive Value Carnac(20): 0.915 Contrafold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.610 Carnac(20): 0.558 Sensitivity Fold: 0.542 Carnac(20): 0.339 Positive Predictive Value Fold: 0.689 Carnac(20): 0.924 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	28 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.582 HotKnots: 0.577 Sensitivity Carnac(20): 0.371 HotKnots: 0.514 Positive Predictive Value Carnac(20): 0.915 HotKnots: 0.652 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.95331270335e-05	9 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Carnac(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.524 Carnac(20): 0.341 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.571 Carnac(20): 0.560 Sensitivity IPknot: 0.463 Carnac(20): 0.367 Positive Predictive Value IPknot: 0.710 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.588 Carnac(20): 0.584 Sensitivity MaxExpect: 0.516 Carnac(20): 0.375 Positive Predictive Value MaxExpect: 0.675 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.61414169632e-05	28 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.585 Carnac(20): 0.582 Sensitivity UNAFold: 0.512 Carnac(20): 0.371 Positive Predictive Value UNAFold: 0.672 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0014549156141	5 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.579 Carnac(20): 0.476 Sensitivity ContextFold: 0.443 Carnac(20): 0.281 Positive Predictive Value ContextFold: 0.763 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.582 RNAshapes: 0.577 Sensitivity Carnac(20): 0.371 RNAshapes: 0.506 Positive Predictive Value Carnac(20): 0.915 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000279205044453	28 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.582 RNAfold: 0.567 Sensitivity Carnac(20): 0.371 RNAfold: 0.503 Positive Predictive Value Carnac(20): 0.915 RNAfold: 0.644 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.29540574715e-07	28 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.582 PknotsRG: 0.579 Sensitivity Carnac(20): 0.371 PknotsRG: 0.516 Positive Predictive Value Carnac(20): 0.915 PknotsRG: 0.653 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00230851584557	26 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Carnac(20): 0.584 Sensitivity CentroidAlifold(seed): 0.430 Carnac(20): 0.375 Positive Predictive Value CentroidAlifold(seed): 0.923 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.586 Carnac(20): 0.558 Sensitivity ProbKnot: 0.529 Carnac(20): 0.339 Positive Predictive Value ProbKnot: 0.653 Carnac(20): 0.924 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	28 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.582 Carnac(20): 0.582 Sensitivity Murlet(20): 0.423 Carnac(20): 0.371 Positive Predictive Value Murlet(20): 0.804 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.379481211626		+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.576 Afold: 0.518 Sensitivity Carnac(20): 0.361 Afold: 0.469 Positive Predictive Value Carnac(20): 0.922 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.582 RNAsubopt: 0.550 Sensitivity Carnac(20): 0.371 RNAsubopt: 0.492 Positive Predictive Value Carnac(20): 0.915 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.608 Carnac(20): 0.588 Sensitivity Cylofold: 0.523 Carnac(20): 0.373 Positive Predictive Value Cylofold: 0.712 Carnac(20): 0.934 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.3438379157e-07	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.582 McQFold: 0.524 Sensitivity Carnac(20): 0.371 McQFold: 0.454 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	- RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Carnac(20): 0.523 Sensitivity RNAalifold(seed): 0.356 Carnac(20): 0.289 Positive Predictive Value RNAalifold(seed): 0.923 Carnac(20): 0.949 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.596 Pknots: 0.530 Sensitivity Carnac(20): 0.391 Pknots: 0.483 Positive Predictive Value Carnac(20): 0.913 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ 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: 1.49381627234e-08	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Carnac(20): 0.574 Sensitivity RNASampler(seed): 0.444 Carnac(20): 0.343 Positive Predictive Value RNASampler(seed): 0.768 Carnac(20): 0.965 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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 RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.586 RSpredict(20): 0.547 Sensitivity Carnac(20): 0.377 RSpredict(20): 0.428 Positive Predictive Value Carnac(20): 0.916 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.582 Mastr(20): 0.525 Sensitivity Carnac(20): 0.371 Mastr(20): 0.346 Positive Predictive Value Carnac(20): 0.915 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.582 Vsfold4: 0.450 Sensitivity Carnac(20): 0.371 Vsfold4: 0.379 Positive Predictive Value Carnac(20): 0.915 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.476 RNASLOpt: 0.467 Sensitivity Carnac(20): 0.281 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.810 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	= Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.521 Carnac(20): 0.513 Sensitivity Multilign(20): 0.428 Carnac(20): 0.307 Positive Predictive Value Multilign(20): 0.643 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0111379505373	? Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.560 RNAwolf: 0.364 Sensitivity Carnac(20): 0.367 RNAwolf: 0.333 Positive Predictive Value Carnac(20): 0.861 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.534 Murlet(seed): 0.491 Sensitivity Carnac(20): 0.302 Murlet(seed): 0.269 Positive Predictive Value Carnac(20): 0.951 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.615 MCFold: 0.421 Sensitivity Carnac(20): 0.413 MCFold: 0.445 Positive Predictive Value Carnac(20): 0.921 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.582 Vsfold5: 0.406 Sensitivity Carnac(20): 0.371 Vsfold5: 0.347 Positive Predictive Value Carnac(20): 0.915 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.617 RDfolder: 0.529 Sensitivity Carnac(20): 0.422 RDfolder: 0.431 Positive Predictive Value Carnac(20): 0.908 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.586 RSpredict(seed): 0.249 Sensitivity Carnac(20): 0.377 RSpredict(seed): 0.110 Positive Predictive Value Carnac(20): 0.916 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.560 PPfold(seed): 0.026 Sensitivity Carnac(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.506 NanoFolder: 0.316 Sensitivity Carnac(20): 0.318 NanoFolder: 0.324 Positive Predictive Value Carnac(20): 0.810 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.582 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.371 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.915 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-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	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Carnac(20): 0.566 Sensitivity Multilign(seed): 0.543 Carnac(20): 0.362 Positive Predictive Value Multilign(seed): 0.852 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(seed): 0.557 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Carnac(20): 0.540 Sensitivity TurboFold(20): 0.500 Carnac(20): 0.341 Positive Predictive Value TurboFold(20): 0.775 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Carnac(20): 0.523 Sensitivity TurboFold(seed): 0.490 Carnac(20): 0.316 Positive Predictive Value TurboFold(seed): 0.729 Carnac(20): 0.874 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.663 Carnac(20): 0.540 Sensitivity PPfold(20): 0.514 Carnac(20): 0.341 Positive Predictive Value PPfold(20): 0.861 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.583 Carnac(seed): 0.197 Sensitivity Carnac(20): 0.366 Carnac(seed): 0.039 Positive Predictive Value Carnac(20): 0.932 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
Afold	32 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.664 Afold: 0.570 Sensitivity MXScarna(seed): 0.554 Afold: 0.534 Positive Predictive Value MXScarna(seed): 0.799 Afold: 0.613 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	80 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.565 Afold: 0.500 Sensitivity CentroidFold: 0.485 Afold: 0.463 Positive Predictive Value CentroidFold: 0.658 Afold: 0.541 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.641 Afold: 0.513 Sensitivity CentroidAlifold(20): 0.484 Afold: 0.472 Positive Predictive Value CentroidAlifold(20): 0.852 Afold: 0.563 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	19 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.597 Afold: 0.518 Sensitivity RNAalifold(20): 0.451 Afold: 0.469 Positive Predictive Value RNAalifold(20): 0.793 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	19 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.597 Afold: 0.518 Sensitivity RNASampler(20): 0.452 Afold: 0.469 Positive Predictive Value RNASampler(20): 0.792 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	95 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.515 Afold: 0.491 Sensitivity Sfold: 0.438 Afold: 0.446 Positive Predictive Value Sfold: 0.604 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.602 Afold: 0.518 Sensitivity MXScarna(20): 0.506 Afold: 0.469 Positive Predictive Value MXScarna(20): 0.719 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	95 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.567 Afold: 0.491 Sensitivity Contrafold: 0.505 Afold: 0.446 Positive Predictive Value Contrafold: 0.637 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Fold vs Afold Matthews Correlation Coefficient Fold: 0.693 Afold: 0.672 Sensitivity Fold: 0.643 Afold: 0.629 Positive Predictive Value Fold: 0.751 Afold: 0.722 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.670 Afold: 0.647 Sensitivity HotKnots: 0.614 Afold: 0.595 Positive Predictive Value HotKnots: 0.735 Afold: 0.709 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 Afold: 0.664 Sensitivity CentroidHomfold‑LAST: 0.542 Afold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.834 Afold: 0.726 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.369701004532	24 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.728 Afold: 0.670 Sensitivity IPknot: 0.628 Afold: 0.615 Positive Predictive Value IPknot: 0.848 Afold: 0.738 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	73 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.611 Afold: 0.564 Sensitivity MaxExpect: 0.538 Afold: 0.505 Positive Predictive Value MaxExpect: 0.695 Afold: 0.630 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	95 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.495 Afold: 0.491 Sensitivity UNAFold: 0.444 Afold: 0.446 Positive Predictive Value UNAFold: 0.551 Afold: 0.541 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 2.23046259944e-06	18 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.709 Afold: 0.677 Sensitivity ContextFold: 0.610 Afold: 0.624 Positive Predictive Value ContextFold: 0.831 Afold: 0.740 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.67407019774e-08	92 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.659 Afold: 0.647 Sensitivity RNAshapes: 0.596 Afold: 0.595 Positive Predictive Value RNAshapes: 0.733 Afold: 0.709 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 1.97386617324e-07	95 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.491 RNAfold: 0.488 Sensitivity Afold: 0.446 RNAfold: 0.443 Positive Predictive Value Afold: 0.541 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 0.00324372766907	95 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.491 PknotsRG: 0.477 Sensitivity Afold: 0.446 PknotsRG: 0.434 Positive Predictive Value Afold: 0.541 PknotsRG: 0.526 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.85233844192e-08	31 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.601 Afold: 0.566 Sensitivity CentroidAlifold(seed): 0.424 Afold: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.854 Afold: 0.608 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.62644058675e-08	50 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.652 Afold: 0.647 Sensitivity ProbKnot: 0.612 Afold: 0.605 Positive Predictive Value ProbKnot: 0.699 Afold: 0.695 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 0.000186465496926	19 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.541 Afold: 0.518 Sensitivity Murlet(20): 0.391 Afold: 0.469 Positive Predictive Value Murlet(20): 0.753 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.45559089896e-08	19 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.576 Afold: 0.518 Sensitivity Carnac(20): 0.361 Afold: 0.469 Positive Predictive Value Carnac(20): 0.922 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08		= Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.647 RNAsubopt: 0.645 Sensitivity Afold: 0.595 RNAsubopt: 0.591 Positive Predictive Value Afold: 0.709 RNAsubopt: 0.710 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.00778217989366	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.712 Cylofold: 0.669 Sensitivity Afold: 0.655 Cylofold: 0.582 Positive Predictive Value Afold: 0.780 Cylofold: 0.775 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.489 McQFold: 0.428 Sensitivity Afold: 0.444 McQFold: 0.334 Positive Predictive Value Afold: 0.539 McQFold: 0.548 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.607 RNAalifold(seed): 0.571 Sensitivity Afold: 0.571 RNAalifold(seed): 0.380 Positive Predictive Value Afold: 0.649 RNAalifold(seed): 0.860 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Afold vs Pknots Matthews Correlation Coefficient Afold: 0.678 Pknots: 0.665 Sensitivity Afold: 0.617 Pknots: 0.611 Positive Predictive Value Afold: 0.752 Pknots: 0.731 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 6.06606238843e-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	+ Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.714 RNASampler(seed): 0.680 Sensitivity Afold: 0.668 RNASampler(seed): 0.550 Positive Predictive Value Afold: 0.766 RNASampler(seed): 0.845 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ 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: 3.27388928538e-08	- RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.551 Afold: 0.521 Sensitivity RSpredict(20): 0.456 Afold: 0.479 Positive Predictive Value RSpredict(20): 0.670 Afold: 0.571 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 4.98606912064e-08	= Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.523 Afold: 0.518 Sensitivity Mastr(20): 0.343 Afold: 0.469 Positive Predictive Value Mastr(20): 0.800 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.0190329081063	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.647 Vsfold4: 0.572 Sensitivity Afold: 0.595 Vsfold4: 0.494 Positive Predictive Value Afold: 0.709 Vsfold4: 0.670 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.677 RNASLOpt: 0.646 Sensitivity Afold: 0.624 RNASLOpt: 0.572 Positive Predictive Value Afold: 0.740 RNASLOpt: 0.736 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.503 Multilign(20): 0.412 Sensitivity Afold: 0.459 Multilign(20): 0.338 Positive Predictive Value Afold: 0.557 Multilign(20): 0.510 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.670 RNAwolf: 0.595 Sensitivity Afold: 0.615 RNAwolf: 0.563 Positive Predictive Value Afold: 0.738 RNAwolf: 0.636 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.690 Murlet(seed): 0.553 Sensitivity Afold: 0.630 Murlet(seed): 0.367 Positive Predictive Value Afold: 0.760 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.688 MCFold: 0.617 Sensitivity Afold: 0.631 MCFold: 0.636 Positive Predictive Value Afold: 0.757 MCFold: 0.606 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.646 Vsfold5: 0.543 Sensitivity Afold: 0.594 Vsfold5: 0.473 Positive Predictive Value Afold: 0.708 Vsfold5: 0.629 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.712 RDfolder: 0.629 Sensitivity Afold: 0.648 RDfolder: 0.529 Positive Predictive Value Afold: 0.789 RDfolder: 0.758 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.570 RSpredict(seed): 0.374 Sensitivity Afold: 0.534 RSpredict(seed): 0.208 Positive Predictive Value Afold: 0.613 RSpredict(seed): 0.677 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.489 PPfold(seed): 0.187 Sensitivity Afold: 0.443 PPfold(seed): 0.066 Positive Predictive Value Afold: 0.547 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.683 NanoFolder: 0.548 Sensitivity Afold: 0.643 NanoFolder: 0.576 Positive Predictive Value Afold: 0.731 NanoFolder: 0.529 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.566 Mastr(seed): 0.304 Sensitivity Afold: 0.525 Mastr(seed): 0.103 Positive Predictive Value Afold: 0.614 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 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 Multilign(seed) Matthews Correlation Coefficient Afold: 0.781 Multilign(seed): 0.610 Sensitivity Afold: 0.676 Multilign(seed): 0.500 Positive Predictive Value Afold: 0.909 Multilign(seed): 0.755 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 Afold: 0.389 Sensitivity PETfold_pre2.0(seed): 0.403 Afold: 0.375 Positive Predictive Value PETfold_pre2.0(seed): 0.644 Afold: 0.409 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.593 Afold: 0.564 Sensitivity TurboFold(20): 0.491 Afold: 0.519 Positive Predictive Value TurboFold(20): 0.722 Afold: 0.618 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.333 Afold: 0.311 Sensitivity PETfold_pre2.0(20): 0.250 Afold: 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.320 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? 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	? Afold vs PPfold(20) Matthews Correlation Coefficient Afold: 0.564 PPfold(20): 0.522 Sensitivity Afold: 0.519 PPfold(20): 0.377 Positive Predictive Value Afold: 0.618 PPfold(20): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.678 Carnac(seed): 0.311 Sensitivity Afold: 0.624 Carnac(seed): 0.097 Positive Predictive Value Afold: 0.742 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNAsubopt	44 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.673 RNAsubopt: 0.570 Sensitivity MXScarna(seed): 0.562 RNAsubopt: 0.521 Positive Predictive Value MXScarna(seed): 0.809 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.676 RNAsubopt: 0.638 Sensitivity CentroidFold: 0.591 RNAsubopt: 0.580 Positive Predictive Value CentroidFold: 0.777 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RNAsubopt: 0.560 Sensitivity CentroidAlifold(20): 0.520 RNAsubopt: 0.503 Positive Predictive Value CentroidAlifold(20): 0.892 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAsubopt: 0.550 Sensitivity RNAalifold(20): 0.491 RNAsubopt: 0.492 Positive Predictive Value RNAalifold(20): 0.849 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.634 RNAsubopt: 0.550 Sensitivity RNASampler(20): 0.477 RNAsubopt: 0.492 Positive Predictive Value RNASampler(20): 0.844 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	118 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.669 RNAsubopt: 0.635 Sensitivity Sfold: 0.581 RNAsubopt: 0.574 Positive Predictive Value Sfold: 0.775 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.628 RNAsubopt: 0.550 Sensitivity MXScarna(20): 0.523 RNAsubopt: 0.492 Positive Predictive Value MXScarna(20): 0.757 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	118 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.660 RNAsubopt: 0.635 Sensitivity Contrafold: 0.592 RNAsubopt: 0.574 Positive Predictive Value Contrafold: 0.740 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.679 RNAsubopt: 0.663 Sensitivity Fold: 0.618 RNAsubopt: 0.605 Positive Predictive Value Fold: 0.751 RNAsubopt: 0.732 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.662 RNAsubopt: 0.635 Sensitivity HotKnots: 0.600 RNAsubopt: 0.574 Positive Predictive Value HotKnots: 0.736 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 RNAsubopt: 0.613 Sensitivity CentroidHomfold‑LAST: 0.515 RNAsubopt: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNAsubopt: 0.697 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.675 RNAsubopt: 0.604 Sensitivity IPknot: 0.573 RNAsubopt: 0.538 Positive Predictive Value IPknot: 0.801 RNAsubopt: 0.686 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.653 RNAsubopt: 0.640 Sensitivity MaxExpect: 0.587 RNAsubopt: 0.581 Positive Predictive Value MaxExpect: 0.731 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.85233844192e-08	118 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.664 RNAsubopt: 0.635 Sensitivity UNAFold: 0.595 RNAsubopt: 0.574 Positive Predictive Value UNAFold: 0.747 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.705 RNAsubopt: 0.584 Sensitivity ContextFold: 0.594 RNAsubopt: 0.525 Positive Predictive Value ContextFold: 0.843 RNAsubopt: 0.658 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.650 RNAsubopt: 0.635 Sensitivity RNAshapes: 0.580 RNAsubopt: 0.574 Positive Predictive Value RNAshapes: 0.733 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.651 RNAsubopt: 0.635 Sensitivity RNAfold: 0.587 RNAsubopt: 0.574 Positive Predictive Value RNAfold: 0.726 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.646 RNAsubopt: 0.635 Sensitivity PknotsRG: 0.585 RNAsubopt: 0.574 Positive Predictive Value PknotsRG: 0.718 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.85233844192e-08	43 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RNAsubopt: 0.567 Sensitivity CentroidAlifold(seed): 0.419 RNAsubopt: 0.519 Positive Predictive Value CentroidAlifold(seed): 0.878 RNAsubopt: 0.624 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.646 RNAsubopt: 0.644 Sensitivity ProbKnot: 0.597 RNAsubopt: 0.587 Positive Predictive Value ProbKnot: 0.703 RNAsubopt: 0.712 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.0782705756228	28 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.582 RNAsubopt: 0.550 Sensitivity Murlet(20): 0.423 RNAsubopt: 0.492 Positive Predictive Value Murlet(20): 0.804 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.582 RNAsubopt: 0.550 Sensitivity Carnac(20): 0.371 RNAsubopt: 0.492 Positive Predictive Value Carnac(20): 0.915 RNAsubopt: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	92 Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.647 RNAsubopt: 0.645 Sensitivity Afold: 0.595 RNAsubopt: 0.591 Positive Predictive Value Afold: 0.709 RNAsubopt: 0.710 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.00778217989366		+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.682 Cylofold: 0.648 Sensitivity RNAsubopt: 0.609 Cylofold: 0.559 Positive Predictive Value RNAsubopt: 0.768 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.633 McQFold: 0.620 Sensitivity RNAsubopt: 0.572 McQFold: 0.540 Positive Predictive Value RNAsubopt: 0.706 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 4.1569883686e-08	- RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.593 RNAsubopt: 0.582 Sensitivity RNAalifold(seed): 0.397 RNAsubopt: 0.537 Positive Predictive Value RNAalifold(seed): 0.887 RNAsubopt: 0.636 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 2.34788726255e-07	+ RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.655 Pknots: 0.634 Sensitivity RNAsubopt: 0.587 Pknots: 0.575 Positive Predictive Value RNAsubopt: 0.738 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-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	- RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.673 RNAsubopt: 0.636 Sensitivity RNASampler(seed): 0.535 RNAsubopt: 0.595 Positive Predictive Value RNASampler(seed): 0.851 RNAsubopt: 0.685 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-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: 0.0360075305827	+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.564 RSpredict(20): 0.547 Sensitivity RNAsubopt: 0.507 RSpredict(20): 0.428 Positive Predictive Value RNAsubopt: 0.631 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.64876692942e-07	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.550 Mastr(20): 0.525 Sensitivity RNAsubopt: 0.492 Mastr(20): 0.346 Positive Predictive Value RNAsubopt: 0.619 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.6710542315e-07	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.635 Vsfold4: 0.562 Sensitivity RNAsubopt: 0.574 Vsfold4: 0.481 Positive Predictive Value RNAsubopt: 0.708 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.591 RNAsubopt: 0.584 Sensitivity RNASLOpt: 0.498 RNAsubopt: 0.525 Positive Predictive Value RNASLOpt: 0.709 RNAsubopt: 0.658 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.000579628272742	+ RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.569 Multilign(20): 0.521 Sensitivity RNAsubopt: 0.497 Multilign(20): 0.428 Positive Predictive Value RNAsubopt: 0.657 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.604 RNAwolf: 0.512 Sensitivity RNAsubopt: 0.538 RNAwolf: 0.479 Positive Predictive Value RNAsubopt: 0.686 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.624 Murlet(seed): 0.539 Sensitivity RNAsubopt: 0.562 Murlet(seed): 0.337 Positive Predictive Value RNAsubopt: 0.698 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.671 MCFold: 0.577 Sensitivity RNAsubopt: 0.605 MCFold: 0.597 Positive Predictive Value RNAsubopt: 0.750 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.634 Vsfold5: 0.528 Sensitivity RNAsubopt: 0.573 Vsfold5: 0.458 Positive Predictive Value RNAsubopt: 0.707 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.691 RDfolder: 0.596 Sensitivity RNAsubopt: 0.614 RDfolder: 0.495 Positive Predictive Value RNAsubopt: 0.784 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(seed): 0.314 Sensitivity RNAsubopt: 0.521 RSpredict(seed): 0.161 Positive Predictive Value RNAsubopt: 0.627 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.500 PPfold(seed): 0.102 Sensitivity RNAsubopt: 0.429 PPfold(seed): 0.020 Positive Predictive Value RNAsubopt: 0.591 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.575 NanoFolder: 0.490 Sensitivity RNAsubopt: 0.517 NanoFolder: 0.495 Positive Predictive Value RNAsubopt: 0.646 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.560 Mastr(seed): 0.258 Sensitivity RNAsubopt: 0.511 Mastr(seed): 0.075 Positive Predictive Value RNAsubopt: 0.619 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.593 RNAsubopt: 0.588 Sensitivity Multilign(seed): 0.475 RNAsubopt: 0.494 Positive Predictive Value Multilign(seed): 0.750 RNAsubopt: 0.709 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAsubopt: 0.431 Sensitivity PETfold_pre2.0(seed): 0.551 RNAsubopt: 0.378 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAsubopt: 0.500 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.620 RNAsubopt: 0.583 Sensitivity TurboFold(20): 0.500 RNAsubopt: 0.507 Positive Predictive Value TurboFold(20): 0.775 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAsubopt: 0.477 Sensitivity PETfold_pre2.0(20): 0.497 RNAsubopt: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAsubopt: 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): 0.550 RNAsubopt: 0.530 Sensitivity TurboFold(seed): 0.456 RNAsubopt: 0.463 Positive Predictive Value TurboFold(seed): 0.672 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.663 RNAsubopt: 0.583 Sensitivity PPfold(20): 0.514 RNAsubopt: 0.507 Positive Predictive Value PPfold(20): 0.861 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.636 Carnac(seed): 0.260 Sensitivity RNAsubopt: 0.575 Carnac(seed): 0.068 Positive Predictive Value RNAsubopt: 0.708 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
Cylofold	21 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.676 Cylofold: 0.640 Sensitivity MXScarna(seed): 0.565 Cylofold: 0.553 Positive Predictive Value MXScarna(seed): 0.814 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.32337795675e-08	63 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.711 Cylofold: 0.648 Sensitivity CentroidFold: 0.615 Cylofold: 0.559 Positive Predictive Value CentroidFold: 0.827 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.703 Cylofold: 0.608 Sensitivity CentroidAlifold(20): 0.536 Cylofold: 0.523 Positive Predictive Value CentroidAlifold(20): 0.926 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	14 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.668 Cylofold: 0.608 Sensitivity RNAalifold(20): 0.509 Cylofold: 0.523 Positive Predictive Value RNAalifold(20): 0.880 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	14 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.679 Cylofold: 0.608 Sensitivity RNASampler(20): 0.507 Cylofold: 0.523 Positive Predictive Value RNASampler(20): 0.912 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	63 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.697 Cylofold: 0.648 Sensitivity Sfold: 0.603 Cylofold: 0.559 Positive Predictive Value Sfold: 0.810 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.682 Cylofold: 0.608 Sensitivity MXScarna(20): 0.564 Cylofold: 0.523 Positive Predictive Value MXScarna(20): 0.829 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	63 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.696 Cylofold: 0.648 Sensitivity Contrafold: 0.622 Cylofold: 0.559 Positive Predictive Value Contrafold: 0.785 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.701 Cylofold: 0.648 Sensitivity Fold: 0.629 Cylofold: 0.559 Positive Predictive Value Fold: 0.786 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.696 Cylofold: 0.648 Sensitivity HotKnots: 0.629 Cylofold: 0.559 Positive Predictive Value HotKnots: 0.775 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.663 Cylofold: 0.586 Sensitivity CentroidHomfold‑LAST: 0.487 Cylofold: 0.499 Positive Predictive Value CentroidHomfold‑LAST: 0.909 Cylofold: 0.698 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.669 Cylofold: 0.583 Sensitivity IPknot: 0.559 Cylofold: 0.498 Positive Predictive Value IPknot: 0.809 Cylofold: 0.692 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.1503931209e-08	63 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.690 Cylofold: 0.648 Sensitivity MaxExpect: 0.616 Cylofold: 0.559 Positive Predictive Value MaxExpect: 0.778 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.685 Cylofold: 0.648 Sensitivity UNAFold: 0.612 Cylofold: 0.559 Positive Predictive Value UNAFold: 0.772 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.703 Cylofold: 0.578 Sensitivity ContextFold: 0.591 Cylofold: 0.494 Positive Predictive Value ContextFold: 0.842 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	63 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.689 Cylofold: 0.648 Sensitivity RNAshapes: 0.614 Cylofold: 0.559 Positive Predictive Value RNAshapes: 0.779 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.672 Cylofold: 0.648 Sensitivity RNAfold: 0.603 Cylofold: 0.559 Positive Predictive Value RNAfold: 0.756 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.675 Cylofold: 0.648 Sensitivity PknotsRG: 0.609 Cylofold: 0.559 Positive Predictive Value PknotsRG: 0.754 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.640 CentroidAlifold(seed): 0.638 Sensitivity Cylofold: 0.553 CentroidAlifold(seed): 0.437 Positive Predictive Value Cylofold: 0.747 CentroidAlifold(seed): 0.936 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.0974231606503	62 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.679 Cylofold: 0.644 Sensitivity ProbKnot: 0.621 Cylofold: 0.555 Positive Predictive Value ProbKnot: 0.748 Cylofold: 0.755 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.649 Cylofold: 0.608 Sensitivity Murlet(20): 0.483 Cylofold: 0.523 Positive Predictive Value Murlet(20): 0.878 Cylofold: 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	14 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.608 Carnac(20): 0.588 Sensitivity Cylofold: 0.523 Carnac(20): 0.373 Positive Predictive Value Cylofold: 0.712 Carnac(20): 0.934 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.3438379157e-07	43 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.712 Cylofold: 0.669 Sensitivity Afold: 0.655 Cylofold: 0.582 Positive Predictive Value Afold: 0.780 Cylofold: 0.775 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.682 Cylofold: 0.648 Sensitivity RNAsubopt: 0.609 Cylofold: 0.559 Positive Predictive Value RNAsubopt: 0.768 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08		- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.693 Cylofold: 0.645 Sensitivity McQFold: 0.602 Cylofold: 0.555 Positive Predictive Value McQFold: 0.803 Cylofold: 0.755 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.618 RNAalifold(seed): 0.561 Sensitivity Cylofold: 0.537 RNAalifold(seed): 0.373 Positive Predictive Value Cylofold: 0.716 RNAalifold(seed): 0.852 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.19192530585e-08	- Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.661 Cylofold: 0.648 Sensitivity Pknots: 0.597 Cylofold: 0.559 Positive Predictive Value Pknots: 0.739 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ 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 RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.702 RNASampler(seed): 0.613 Sensitivity Cylofold: 0.620 RNASampler(seed): 0.460 Positive Predictive Value Cylofold: 0.800 RNASampler(seed): 0.821 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	= 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: 0.00683149332667	+ Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.608 RSpredict(20): 0.585 Sensitivity Cylofold: 0.523 RSpredict(20): 0.456 Positive Predictive Value Cylofold: 0.712 RSpredict(20): 0.757 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.608 Mastr(20): 0.565 Sensitivity Cylofold: 0.523 Mastr(20): 0.375 Positive Predictive Value Cylofold: 0.712 Mastr(20): 0.856 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.35270341049e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.648 Vsfold4: 0.585 Sensitivity Cylofold: 0.559 Vsfold4: 0.499 Positive Predictive Value Cylofold: 0.758 Vsfold4: 0.694 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.580 Cylofold: 0.578 Sensitivity RNASLOpt: 0.477 Cylofold: 0.494 Positive Predictive Value RNASLOpt: 0.713 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.605145451624	? Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.577 Multilign(20): 0.546 Sensitivity Cylofold: 0.494 Multilign(20): 0.429 Positive Predictive Value Cylofold: 0.684 Multilign(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.583 RNAwolf: 0.511 Sensitivity Cylofold: 0.498 RNAwolf: 0.474 Positive Predictive Value Cylofold: 0.692 RNAwolf: 0.563 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.602 Murlet(seed): 0.502 Sensitivity Cylofold: 0.522 Murlet(seed): 0.300 Positive Predictive Value Cylofold: 0.701 Murlet(seed): 0.849 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.656 MCFold: 0.579 Sensitivity Cylofold: 0.568 MCFold: 0.599 Positive Predictive Value Cylofold: 0.764 MCFold: 0.567 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.648 Vsfold5: 0.546 Sensitivity Cylofold: 0.559 Vsfold5: 0.475 Positive Predictive Value Cylofold: 0.758 Vsfold5: 0.637 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.706 RDfolder: 0.588 Sensitivity Cylofold: 0.613 RDfolder: 0.494 Positive Predictive Value Cylofold: 0.821 RDfolder: 0.710 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.640 RSpredict(seed): 0.274 Sensitivity Cylofold: 0.553 RSpredict(seed): 0.137 Positive Predictive Value Cylofold: 0.747 RSpredict(seed): 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.630 PPfold(seed): 0.128 Sensitivity Cylofold: 0.519 PPfold(seed): 0.022 Positive Predictive Value Cylofold: 0.773 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.620 NanoFolder: 0.546 Sensitivity Cylofold: 0.526 NanoFolder: 0.539 Positive Predictive Value Cylofold: 0.740 NanoFolder: 0.565 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.640 Mastr(seed): 0.263 Sensitivity Cylofold: 0.553 Mastr(seed): 0.070 Positive Predictive Value Cylofold: 0.747 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-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 Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.633 Multilign(seed): 0.593 Sensitivity Cylofold: 0.519 Multilign(seed): 0.475 Positive Predictive Value Cylofold: 0.781 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Cylofold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.521 Cylofold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.821 Cylofold: 0.735 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.689 TurboFold(20): 0.679 Sensitivity Cylofold: 0.576 TurboFold(20): 0.537 Positive Predictive Value Cylofold: 0.830 TurboFold(20): 0.865 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 Cylofold: 0.620 Sensitivity PETfold_pre2.0(20): 0.513 Cylofold: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.872 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.683 TurboFold(seed): 0.598 Sensitivity Cylofold: 0.571 TurboFold(seed): 0.474 Positive Predictive Value Cylofold: 0.824 TurboFold(seed): 0.762 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.702 Cylofold: 0.689 Sensitivity PPfold(20): 0.542 Cylofold: 0.576 Positive Predictive Value PPfold(20): 0.917 Cylofold: 0.830 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.625 Carnac(seed): 0.212 Sensitivity Cylofold: 0.538 Carnac(seed): 0.045 Positive Predictive Value Cylofold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08
McQFold	44 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.673 McQFold: 0.565 Sensitivity MXScarna(seed): 0.562 McQFold: 0.500 Positive Predictive Value MXScarna(seed): 0.809 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.576 McQFold: 0.472 Sensitivity CentroidFold: 0.492 McQFold: 0.365 Positive Predictive Value CentroidFold: 0.674 McQFold: 0.612 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.680 McQFold: 0.531 Sensitivity CentroidAlifold(20): 0.520 McQFold: 0.463 Positive Predictive Value CentroidAlifold(20): 0.892 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.644 McQFold: 0.524 Sensitivity RNAalifold(20): 0.491 McQFold: 0.454 Positive Predictive Value RNAalifold(20): 0.849 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.634 McQFold: 0.524 Sensitivity RNASampler(20): 0.477 McQFold: 0.454 Positive Predictive Value RNASampler(20): 0.844 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	120 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.526 McQFold: 0.443 Sensitivity Sfold: 0.446 McQFold: 0.348 Positive Predictive Value Sfold: 0.620 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.628 McQFold: 0.524 Sensitivity MXScarna(20): 0.523 McQFold: 0.454 Positive Predictive Value MXScarna(20): 0.757 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	120 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.574 McQFold: 0.443 Sensitivity Contrafold: 0.510 McQFold: 0.348 Positive Predictive Value Contrafold: 0.647 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.677 McQFold: 0.646 Sensitivity Fold: 0.616 McQFold: 0.568 Positive Predictive Value Fold: 0.749 McQFold: 0.740 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.661 McQFold: 0.620 Sensitivity HotKnots: 0.598 McQFold: 0.540 Positive Predictive Value HotKnots: 0.735 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 McQFold: 0.616 Sensitivity CentroidHomfold‑LAST: 0.515 McQFold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.873 McQFold: 0.723 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.669 McQFold: 0.604 Sensitivity IPknot: 0.567 McQFold: 0.522 Positive Predictive Value IPknot: 0.796 McQFold: 0.707 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.615 McQFold: 0.519 Sensitivity MaxExpect: 0.538 McQFold: 0.445 Positive Predictive Value MaxExpect: 0.704 McQFold: 0.606 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.507 McQFold: 0.443 Sensitivity UNAFold: 0.453 McQFold: 0.348 Positive Predictive Value UNAFold: 0.568 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.699 McQFold: 0.578 Sensitivity ContextFold: 0.586 McQFold: 0.505 Positive Predictive Value ContextFold: 0.838 McQFold: 0.670 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	117 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.648 McQFold: 0.620 Sensitivity RNAshapes: 0.579 McQFold: 0.540 Positive Predictive Value RNAshapes: 0.731 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.503 McQFold: 0.443 Sensitivity RNAfold: 0.453 McQFold: 0.348 Positive Predictive Value RNAfold: 0.558 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.494 McQFold: 0.443 Sensitivity PknotsRG: 0.446 McQFold: 0.348 Positive Predictive Value PknotsRG: 0.547 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 McQFold: 0.562 Sensitivity CentroidAlifold(seed): 0.419 McQFold: 0.497 Positive Predictive Value CentroidAlifold(seed): 0.878 McQFold: 0.640 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.643 McQFold: 0.633 Sensitivity ProbKnot: 0.595 McQFold: 0.561 Positive Predictive Value ProbKnot: 0.700 McQFold: 0.719 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.37177523642e-07	28 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.582 McQFold: 0.524 Sensitivity Murlet(20): 0.423 McQFold: 0.454 Positive Predictive Value Murlet(20): 0.804 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.582 McQFold: 0.524 Sensitivity Carnac(20): 0.371 McQFold: 0.454 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	94 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.489 McQFold: 0.428 Sensitivity Afold: 0.444 McQFold: 0.334 Positive Predictive Value Afold: 0.539 McQFold: 0.548 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.633 McQFold: 0.620 Sensitivity RNAsubopt: 0.572 McQFold: 0.540 Positive Predictive Value RNAsubopt: 0.706 McQFold: 0.716 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 4.1569883686e-08	62 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.693 Cylofold: 0.645 Sensitivity McQFold: 0.602 Cylofold: 0.555 Positive Predictive Value McQFold: 0.803 Cylofold: 0.755 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.593 McQFold: 0.581 Sensitivity RNAalifold(seed): 0.397 McQFold: 0.523 Positive Predictive Value RNAalifold(seed): 0.887 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.42144954805e-05	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.646 Pknots: 0.632 Sensitivity McQFold: 0.558 Pknots: 0.573 Positive Predictive Value McQFold: 0.754 Pknots: 0.704 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ 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 RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.680 RNASampler(seed): 0.673 Sensitivity McQFold: 0.619 RNASampler(seed): 0.535 Positive Predictive Value McQFold: 0.751 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 7.5822376376e-06	= 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: 0.125446474224	- RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.547 McQFold: 0.536 Sensitivity RSpredict(20): 0.428 McQFold: 0.468 Positive Predictive Value RSpredict(20): 0.702 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000204094570084	= Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.525 McQFold: 0.524 Sensitivity Mastr(20): 0.346 McQFold: 0.454 Positive Predictive Value Mastr(20): 0.800 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.215158657328	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.620 Vsfold4: 0.560 Sensitivity McQFold: 0.540 Vsfold4: 0.479 Positive Predictive Value McQFold: 0.716 Vsfold4: 0.661 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.581 McQFold: 0.578 Sensitivity RNASLOpt: 0.488 McQFold: 0.505 Positive Predictive Value RNASLOpt: 0.699 McQFold: 0.670 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0146580879528	= McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.524 Multilign(20): 0.521 Sensitivity McQFold: 0.455 Multilign(20): 0.428 Positive Predictive Value McQFold: 0.611 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0977095104109	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.604 RNAwolf: 0.502 Sensitivity McQFold: 0.522 RNAwolf: 0.469 Positive Predictive Value McQFold: 0.707 RNAwolf: 0.546 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.647 Murlet(seed): 0.539 Sensitivity McQFold: 0.570 Murlet(seed): 0.337 Positive Predictive Value McQFold: 0.740 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.661 MCFold: 0.575 Sensitivity McQFold: 0.573 MCFold: 0.595 Positive Predictive Value McQFold: 0.769 MCFold: 0.563 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.618 Vsfold5: 0.526 Sensitivity McQFold: 0.539 Vsfold5: 0.456 Positive Predictive Value McQFold: 0.714 Vsfold5: 0.613 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.596 Sensitivity McQFold: 0.604 RDfolder: 0.495 Positive Predictive Value McQFold: 0.831 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.565 RSpredict(seed): 0.314 Sensitivity McQFold: 0.500 RSpredict(seed): 0.161 Positive Predictive Value McQFold: 0.643 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.539 PPfold(seed): 0.102 Sensitivity McQFold: 0.462 PPfold(seed): 0.020 Positive Predictive Value McQFold: 0.637 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.35333035499e-09	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.567 NanoFolder: 0.473 Sensitivity McQFold: 0.500 NanoFolder: 0.479 Positive Predictive Value McQFold: 0.650 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.556 Mastr(seed): 0.258 Sensitivity McQFold: 0.489 Mastr(seed): 0.075 Positive Predictive Value McQFold: 0.636 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.672 Multilign(seed): 0.593 Sensitivity McQFold: 0.563 Multilign(seed): 0.475 Positive Predictive Value McQFold: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 McQFold: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 McQFold: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 McQFold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.620 McQFold: 0.560 Sensitivity TurboFold(20): 0.500 McQFold: 0.486 Positive Predictive Value TurboFold(20): 0.775 McQFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 McQFold: 0.409 Sensitivity PETfold_pre2.0(20): 0.497 McQFold: 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.790 McQFold: 0.466 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.550 McQFold: 0.548 Sensitivity TurboFold(seed): 0.456 McQFold: 0.481 Positive Predictive Value TurboFold(seed): 0.672 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.663 McQFold: 0.560 Sensitivity PPfold(20): 0.514 McQFold: 0.486 Positive Predictive Value PPfold(20): 0.861 McQFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.618 Carnac(seed): 0.260 Sensitivity McQFold: 0.545 Carnac(seed): 0.068 Positive Predictive Value McQFold: 0.706 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	29 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 RNAalifold(seed): 0.593 Sensitivity MXScarna(seed): 0.533 RNAalifold(seed): 0.397 Positive Predictive Value MXScarna(seed): 0.788 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.628 RNAalifold(seed): 0.593 Sensitivity CentroidFold: 0.547 RNAalifold(seed): 0.399 Positive Predictive Value CentroidFold: 0.725 RNAalifold(seed): 0.886 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.638 RNAalifold(seed): 0.573 Sensitivity CentroidAlifold(20): 0.454 RNAalifold(seed): 0.357 Positive Predictive Value CentroidAlifold(20): 0.900 RNAalifold(seed): 0.922 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	18 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.585 RNAalifold(seed): 0.572 Sensitivity RNAalifold(20): 0.420 RNAalifold(seed): 0.356 Positive Predictive Value RNAalifold(20): 0.818 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54600035591e-07	18 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.584 RNAalifold(seed): 0.572 Sensitivity RNASampler(20): 0.427 RNAalifold(seed): 0.356 Positive Predictive Value RNASampler(20): 0.803 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	29 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.629 RNAalifold(seed): 0.593 Sensitivity Sfold: 0.544 RNAalifold(seed): 0.397 Positive Predictive Value Sfold: 0.730 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.603 RNAalifold(seed): 0.572 Sensitivity MXScarna(20): 0.488 RNAalifold(seed): 0.356 Positive Predictive Value MXScarna(20): 0.749 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	29 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.608 RNAalifold(seed): 0.593 Sensitivity Contrafold: 0.552 RNAalifold(seed): 0.397 Positive Predictive Value Contrafold: 0.673 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.62644058675e-08	22 Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.588 RNAalifold(seed): 0.571 Sensitivity Fold: 0.543 RNAalifold(seed): 0.375 Positive Predictive Value Fold: 0.640 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 7.71892784613e-07	29 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.620 RNAalifold(seed): 0.593 Sensitivity HotKnots: 0.571 RNAalifold(seed): 0.397 Positive Predictive Value HotKnots: 0.677 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	8 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.573 RNAalifold(seed): 0.529 Sensitivity CentroidHomfold‑LAST: 0.450 RNAalifold(seed): 0.349 Positive Predictive Value CentroidHomfold‑LAST: 0.736 RNAalifold(seed): 0.808 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.523 IPknot: 0.505 Sensitivity RNAalifold(seed): 0.344 IPknot: 0.402 Positive Predictive Value RNAalifold(seed): 0.800 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	27 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.588 MaxExpect: 0.584 Sensitivity RNAalifold(seed): 0.394 MaxExpect: 0.529 Positive Predictive Value RNAalifold(seed): 0.881 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.14339240505	29 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.609 RNAalifold(seed): 0.593 Sensitivity UNAFold: 0.551 RNAalifold(seed): 0.397 Positive Predictive Value UNAFold: 0.675 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.59469103578e-08	5 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.488 RNAalifold(seed): 0.472 Sensitivity ContextFold: 0.376 RNAalifold(seed): 0.293 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	29 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.627 RNAalifold(seed): 0.593 Sensitivity RNAshapes: 0.567 RNAalifold(seed): 0.397 Positive Predictive Value RNAshapes: 0.696 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.620 RNAalifold(seed): 0.593 Sensitivity RNAfold: 0.568 RNAalifold(seed): 0.397 Positive Predictive Value RNAfold: 0.680 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.06544643719e-08	29 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.621 RNAalifold(seed): 0.593 Sensitivity PknotsRG: 0.571 RNAalifold(seed): 0.397 Positive Predictive Value PknotsRG: 0.678 RNAalifold(seed): 0.887 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.660 RNAalifold(seed): 0.593 Sensitivity CentroidAlifold(seed): 0.504 RNAalifold(seed): 0.399 Positive Predictive Value CentroidAlifold(seed): 0.866 RNAalifold(seed): 0.886 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.520 RNAalifold(seed): 0.519 Sensitivity ProbKnot: 0.487 RNAalifold(seed): 0.320 Positive Predictive Value ProbKnot: 0.559 RNAalifold(seed): 0.843 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.486848903635	18 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Murlet(20): 0.524 Sensitivity RNAalifold(seed): 0.356 Murlet(20): 0.357 Positive Predictive Value RNAalifold(seed): 0.923 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.57327336088e-08	18 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Carnac(20): 0.523 Sensitivity RNAalifold(seed): 0.356 Carnac(20): 0.289 Positive Predictive Value RNAalifold(seed): 0.923 Carnac(20): 0.949 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	23 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.607 RNAalifold(seed): 0.571 Sensitivity Afold: 0.571 RNAalifold(seed): 0.380 Positive Predictive Value Afold: 0.649 RNAalifold(seed): 0.860 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	29 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.593 RNAsubopt: 0.582 Sensitivity RNAalifold(seed): 0.397 RNAsubopt: 0.537 Positive Predictive Value RNAalifold(seed): 0.887 RNAsubopt: 0.636 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 2.34788726255e-07	14 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.618 RNAalifold(seed): 0.561 Sensitivity Cylofold: 0.537 RNAalifold(seed): 0.373 Positive Predictive Value Cylofold: 0.716 RNAalifold(seed): 0.852 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.19192530585e-08	29 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.593 McQFold: 0.581 Sensitivity RNAalifold(seed): 0.397 McQFold: 0.523 Positive Predictive Value RNAalifold(seed): 0.887 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.42144954805e-05		= RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.636 Pknots: 0.636 Sensitivity RNAalifold(seed): 0.449 Pknots: 0.588 Positive Predictive Value RNAalifold(seed): 0.905 Pknots: 0.693 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.475054585957	- 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: 2.45805449719e-08	- RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 RNAalifold(seed): 0.646 Sensitivity RNASampler(seed): 0.535 RNAalifold(seed): 0.483 Positive Predictive Value RNASampler(seed): 0.851 RNAalifold(seed): 0.868 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	? 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 RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 RSpredict(20): 0.480 Sensitivity RNAalifold(seed): 0.356 RSpredict(20): 0.363 Positive Predictive Value RNAalifold(seed): 0.923 RSpredict(20): 0.640 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Mastr(20): 0.415 Sensitivity RNAalifold(seed): 0.356 Mastr(20): 0.221 Positive Predictive Value RNAalifold(seed): 0.923 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.593 Vsfold4: 0.498 Sensitivity RNAalifold(seed): 0.397 Vsfold4: 0.432 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNASLOpt: 0.390 Sensitivity RNAalifold(seed): 0.293 RNASLOpt: 0.323 Positive Predictive Value RNAalifold(seed): 0.765 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Multilign(20): 0.468 Sensitivity RNAalifold(seed): 0.355 Multilign(20): 0.378 Positive Predictive Value RNAalifold(seed): 0.927 Multilign(20): 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.523 RNAwolf: 0.370 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.344 Positive Predictive Value RNAalifold(seed): 0.800 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Murlet(seed): 0.539 Sensitivity RNAalifold(seed): 0.460 Murlet(seed): 0.337 Positive Predictive Value RNAalifold(seed): 0.905 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.629 MCFold: 0.547 Sensitivity RNAalifold(seed): 0.443 MCFold: 0.562 Positive Predictive Value RNAalifold(seed): 0.898 MCFold: 0.538 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.593 Vsfold5: 0.481 Sensitivity RNAalifold(seed): 0.397 Vsfold5: 0.421 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold5: 0.555 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.668 RDfolder: 0.603 Sensitivity RNAalifold(seed): 0.509 RDfolder: 0.493 Positive Predictive Value RNAalifold(seed): 0.884 RDfolder: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 RSpredict(seed): 0.404 Sensitivity RNAalifold(seed): 0.397 RSpredict(seed): 0.232 Positive Predictive Value RNAalifold(seed): 0.887 RSpredict(seed): 0.708 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 PPfold(seed): 0.133 Sensitivity RNAalifold(seed): 0.344 PPfold(seed): 0.033 Positive Predictive Value RNAalifold(seed): 0.800 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.459 NanoFolder: 0.280 Sensitivity RNAalifold(seed): 0.289 NanoFolder: 0.298 Positive Predictive Value RNAalifold(seed): 0.733 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Mastr(seed): 0.319 Sensitivity RNAalifold(seed): 0.397 Mastr(seed): 0.114 Positive Predictive Value RNAalifold(seed): 0.887 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-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	? Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 RNAalifold(seed): 0.550 Sensitivity Multilign(seed): 0.475 RNAalifold(seed): 0.399 Positive Predictive Value Multilign(seed): 0.750 RNAalifold(seed): 0.768 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 RNAalifold(seed): 0.472 Sensitivity PETfold_pre2.0(seed): 0.459 RNAalifold(seed): 0.293 Positive Predictive Value PETfold_pre2.0(seed): 0.726 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 TurboFold(20): 0.590 Sensitivity RNAalifold(seed): 0.383 TurboFold(20): 0.469 Positive Predictive Value RNAalifold(seed): 0.920 TurboFold(20): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.586 PETfold_pre2.0(20): 0.527 Sensitivity RNAalifold(seed): 0.345 PETfold_pre2.0(20): 0.407 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.529 TurboFold(seed): 0.517 Sensitivity RNAalifold(seed): 0.349 TurboFold(seed): 0.428 Positive Predictive Value RNAalifold(seed): 0.808 TurboFold(seed): 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.605 RNAalifold(seed): 0.591 Sensitivity PPfold(20): 0.455 RNAalifold(seed): 0.383 Positive Predictive Value PPfold(20): 0.812 RNAalifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Carnac(seed): 0.287 Sensitivity RNAalifold(seed): 0.460 Carnac(seed): 0.083 Positive Predictive Value RNAalifold(seed): 0.905 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08
Pknots	42 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.687 Pknots: 0.615 Sensitivity MXScarna(seed): 0.577 Pknots: 0.562 Positive Predictive Value MXScarna(seed): 0.823 Pknots: 0.679 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	102 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.698 Pknots: 0.637 Sensitivity CentroidFold: 0.608 Pknots: 0.580 Positive Predictive Value CentroidFold: 0.807 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Pknots: 0.542 Sensitivity CentroidAlifold(20): 0.540 Pknots: 0.495 Positive Predictive Value CentroidAlifold(20): 0.893 Pknots: 0.598 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.658 Pknots: 0.530 Sensitivity RNAalifold(20): 0.511 Pknots: 0.483 Positive Predictive Value RNAalifold(20): 0.852 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.655 Pknots: 0.530 Sensitivity RNASampler(20): 0.500 Pknots: 0.483 Positive Predictive Value RNASampler(20): 0.862 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	116 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.691 Pknots: 0.634 Sensitivity Sfold: 0.598 Pknots: 0.575 Positive Predictive Value Sfold: 0.804 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.644 Pknots: 0.530 Sensitivity MXScarna(20): 0.540 Pknots: 0.483 Positive Predictive Value MXScarna(20): 0.773 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	116 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.681 Pknots: 0.634 Sensitivity Contrafold: 0.607 Pknots: 0.575 Positive Predictive Value Contrafold: 0.770 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	80 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.714 Pknots: 0.660 Sensitivity Fold: 0.645 Pknots: 0.599 Positive Predictive Value Fold: 0.796 Pknots: 0.734 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.686 Pknots: 0.634 Sensitivity HotKnots: 0.616 Pknots: 0.575 Positive Predictive Value HotKnots: 0.770 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Pknots: 0.580 Sensitivity CentroidHomfold‑LAST: 0.515 Pknots: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.675 Pknots: 0.574 Sensitivity IPknot: 0.573 Pknots: 0.516 Positive Predictive Value IPknot: 0.801 Pknots: 0.646 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.678 Pknots: 0.635 Sensitivity MaxExpect: 0.606 Pknots: 0.579 Positive Predictive Value MaxExpect: 0.765 Pknots: 0.704 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.688 Pknots: 0.634 Sensitivity UNAFold: 0.612 Pknots: 0.575 Positive Predictive Value UNAFold: 0.780 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.705 Pknots: 0.547 Sensitivity ContextFold: 0.594 Pknots: 0.497 Positive Predictive Value ContextFold: 0.843 Pknots: 0.611 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.674 Pknots: 0.634 Sensitivity RNAshapes: 0.598 Pknots: 0.575 Positive Predictive Value RNAshapes: 0.765 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.674 Pknots: 0.634 Sensitivity RNAfold: 0.602 Pknots: 0.575 Positive Predictive Value RNAfold: 0.760 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.668 Pknots: 0.634 Sensitivity PknotsRG: 0.600 Pknots: 0.575 Positive Predictive Value PknotsRG: 0.751 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.614 Pknots: 0.612 Sensitivity CentroidAlifold(seed): 0.424 Pknots: 0.559 Positive Predictive Value CentroidAlifold(seed): 0.894 Pknots: 0.676 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.226387597291	72 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.680 Pknots: 0.649 Sensitivity ProbKnot: 0.625 Pknots: 0.589 Positive Predictive Value ProbKnot: 0.745 Pknots: 0.722 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.604 Pknots: 0.530 Sensitivity Murlet(20): 0.449 Pknots: 0.483 Positive Predictive Value Murlet(20): 0.818 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.596 Pknots: 0.530 Sensitivity Carnac(20): 0.391 Pknots: 0.483 Positive Predictive Value Carnac(20): 0.913 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	90 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.678 Pknots: 0.665 Sensitivity Afold: 0.617 Pknots: 0.611 Positive Predictive Value Afold: 0.752 Pknots: 0.731 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 6.06606238843e-08	116 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.655 Pknots: 0.634 Sensitivity RNAsubopt: 0.587 Pknots: 0.575 Positive Predictive Value RNAsubopt: 0.738 Pknots: 0.706 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.661 Cylofold: 0.648 Sensitivity Pknots: 0.597 Cylofold: 0.559 Positive Predictive Value Pknots: 0.739 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 6.53888633552e-08	115 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.646 Pknots: 0.632 Sensitivity McQFold: 0.558 Pknots: 0.573 Positive Predictive Value McQFold: 0.754 Pknots: 0.704 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.85233844192e-08	27 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.636 Pknots: 0.636 Sensitivity RNAalifold(seed): 0.449 Pknots: 0.588 Positive Predictive Value RNAalifold(seed): 0.905 Pknots: 0.693 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.475054585957		+ 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	+ Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.701 RNASampler(seed): 0.673 Sensitivity Pknots: 0.668 RNASampler(seed): 0.535 Positive Predictive Value Pknots: 0.739 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.87234834547e-08	- 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: 4.83792096436e-08	= RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.549 Pknots: 0.547 Sensitivity RSpredict(20): 0.428 Pknots: 0.501 Positive Predictive Value RSpredict(20): 0.712 Pknots: 0.604 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0484227593148	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.560 Pknots: 0.530 Sensitivity Mastr(20): 0.395 Pknots: 0.483 Positive Predictive Value Mastr(20): 0.800 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.01557756351e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.634 Vsfold4: 0.584 Sensitivity Pknots: 0.575 Vsfold4: 0.497 Positive Predictive Value Pknots: 0.706 Vsfold4: 0.694 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.591 Pknots: 0.547 Sensitivity RNASLOpt: 0.498 Pknots: 0.497 Positive Predictive Value RNASLOpt: 0.709 Pknots: 0.611 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.48494289621e-08	- Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.521 Pknots: 0.507 Sensitivity Multilign(20): 0.428 Pknots: 0.452 Positive Predictive Value Multilign(20): 0.643 Pknots: 0.577 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.63256991408e-05	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.574 RNAwolf: 0.512 Sensitivity Pknots: 0.516 RNAwolf: 0.479 Positive Predictive Value Pknots: 0.646 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.628 Murlet(seed): 0.539 Sensitivity Pknots: 0.581 Murlet(seed): 0.337 Positive Predictive Value Pknots: 0.685 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.647 MCFold: 0.577 Sensitivity Pknots: 0.591 MCFold: 0.597 Positive Predictive Value Pknots: 0.716 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.633 Vsfold5: 0.547 Sensitivity Pknots: 0.574 Vsfold5: 0.475 Positive Predictive Value Pknots: 0.705 Vsfold5: 0.639 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.596 Sensitivity Pknots: 0.628 RDfolder: 0.495 Positive Predictive Value Pknots: 0.781 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.615 RSpredict(seed): 0.334 Sensitivity Pknots: 0.562 RSpredict(seed): 0.176 Positive Predictive Value Pknots: 0.679 RSpredict(seed): 0.646 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.532 PPfold(seed): 0.102 Sensitivity Pknots: 0.462 PPfold(seed): 0.020 Positive Predictive Value Pknots: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.70361883708e-09	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.515 NanoFolder: 0.490 Sensitivity Pknots: 0.463 NanoFolder: 0.495 Positive Predictive Value Pknots: 0.582 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.65348477097e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.601 Mastr(seed): 0.279 Sensitivity Pknots: 0.547 Mastr(seed): 0.087 Positive Predictive Value Pknots: 0.666 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 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	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.607 Multilign(seed): 0.593 Sensitivity Pknots: 0.519 Multilign(seed): 0.475 Positive Predictive Value Pknots: 0.719 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Pknots: 0.452 Sensitivity PETfold_pre2.0(seed): 0.551 Pknots: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Pknots: 0.518 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.620 Pknots: 0.537 Sensitivity TurboFold(20): 0.500 Pknots: 0.472 Positive Predictive Value TurboFold(20): 0.775 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Pknots: 0.371 Sensitivity PETfold_pre2.0(20): 0.497 Pknots: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Pknots: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.550 Pknots: 0.526 Sensitivity TurboFold(seed): 0.456 Pknots: 0.466 Positive Predictive Value TurboFold(seed): 0.672 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.663 Pknots: 0.537 Sensitivity PPfold(20): 0.514 Pknots: 0.472 Positive Predictive Value PPfold(20): 0.861 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.610 Carnac(seed): 0.260 Sensitivity Pknots: 0.563 Carnac(seed): 0.068 Positive Predictive Value Pknots: 0.666 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
Alterna	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: 5.19332990918e-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	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: 9.16590079822e-09	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: 2.10198558684e-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: 1.66062906821e-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	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: 2.64318034126e-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	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	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	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: 5.23657817852e-08	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: 5.1503931209e-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	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	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: 2.24270395587e-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	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	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	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: 5.10776592382e-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: 1.66062906821e-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: 1.49381627234e-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	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	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: 2.45805449719e-08	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		+ 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: 1.50834591464e-08	= 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: 0.00139331462707	- 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: 1.25253056981e-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: 2.30549897711e-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: 4.83792096436e-08	+ 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: 2.57237423209e-08	? 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	+ 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: 7.8595327961e-05	+ 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: 2.66715895098e-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 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 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 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: 5.23657817852e-08	? 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 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 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 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	? 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	? 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	? 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	? 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	? 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	? 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	+ 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: 3.13260312532e-08
RNASampler(seed)	17 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 MXScarna(seed): 0.672 Sensitivity RNASampler(seed): 0.535 MXScarna(seed): 0.566 Positive Predictive Value RNASampler(seed): 0.851 MXScarna(seed): 0.804 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0250258449044	16 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.707 RNASampler(seed): 0.665 Sensitivity CentroidFold: 0.626 RNASampler(seed): 0.525 Positive Predictive Value CentroidFold: 0.804 RNASampler(seed): 0.846 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.26346675981e-08	7 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.586 RNASampler(seed): 0.560 Sensitivity CentroidAlifold(20): 0.421 RNASampler(seed): 0.421 Positive Predictive Value CentroidAlifold(20): 0.821 RNASampler(seed): 0.750 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RNAalifold(20): 0.514 Sensitivity RNASampler(seed): 0.444 RNAalifold(20): 0.410 Positive Predictive Value RNASampler(seed): 0.768 RNAalifold(20): 0.649 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RNASampler(20): 0.578 Sensitivity RNASampler(seed): 0.444 RNASampler(20): 0.477 Positive Predictive Value RNASampler(seed): 0.768 RNASampler(20): 0.704 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.721 RNASampler(seed): 0.673 Sensitivity Sfold: 0.637 RNASampler(seed): 0.535 Positive Predictive Value Sfold: 0.819 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.91441904741e-08	8 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 MXScarna(20): 0.557 Sensitivity RNASampler(seed): 0.444 MXScarna(20): 0.469 Positive Predictive Value RNASampler(seed): 0.768 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.689 RNASampler(seed): 0.673 Sensitivity Contrafold: 0.630 RNASampler(seed): 0.535 Positive Predictive Value Contrafold: 0.759 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.44851456278e-08	12 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.662 Fold: 0.642 Sensitivity RNASampler(seed): 0.525 Fold: 0.607 Positive Predictive Value RNASampler(seed): 0.839 Fold: 0.684 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.78614631659e-08	17 HotKnots vs RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.699 RNASampler(seed): 0.673 Sensitivity HotKnots: 0.653 RNASampler(seed): 0.535 Positive Predictive Value HotKnots: 0.753 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.52299983238e-08	5 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.504 CentroidHomfold‑LAST: 0.496 Sensitivity RNASampler(seed): 0.369 CentroidHomfold‑LAST: 0.403 Positive Predictive Value RNASampler(seed): 0.696 CentroidHomfold‑LAST: 0.619 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.493 RNASampler(seed): 0.471 Sensitivity IPknot: 0.395 RNASampler(seed): 0.341 Positive Predictive Value IPknot: 0.622 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	15 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.662 MaxExpect: 0.646 Sensitivity RNASampler(seed): 0.529 MaxExpect: 0.599 Positive Predictive Value RNASampler(seed): 0.835 MaxExpect: 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.78784325942e-08	17 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.690 RNASampler(seed): 0.673 Sensitivity UNAFold: 0.635 RNASampler(seed): 0.535 Positive Predictive Value UNAFold: 0.754 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	2 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.351 RNASampler(seed): 0.198 Sensitivity ContextFold: 0.283 RNASampler(seed): 0.151 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	17 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.696 RNASampler(seed): 0.673 Sensitivity RNAshapes: 0.641 RNASampler(seed): 0.535 Positive Predictive Value RNAshapes: 0.760 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.21817282663e-08	17 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.712 RNASampler(seed): 0.673 Sensitivity RNAfold: 0.659 RNASampler(seed): 0.535 Positive Predictive Value RNAfold: 0.773 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.00627773251e-08	17 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.687 RNASampler(seed): 0.673 Sensitivity PknotsRG: 0.637 RNASampler(seed): 0.535 Positive Predictive Value PknotsRG: 0.745 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.20802062638e-07	16 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.668 RNASampler(seed): 0.665 Sensitivity CentroidAlifold(seed): 0.532 RNASampler(seed): 0.525 Positive Predictive Value CentroidAlifold(seed): 0.844 RNASampler(seed): 0.846 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.673410491699	8 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.568 ProbKnot: 0.543 Sensitivity RNASampler(seed): 0.429 ProbKnot: 0.528 Positive Predictive Value RNASampler(seed): 0.758 ProbKnot: 0.564 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Murlet(20): 0.496 Sensitivity RNASampler(seed): 0.444 Murlet(20): 0.385 Positive Predictive Value RNASampler(seed): 0.768 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Carnac(20): 0.574 Sensitivity RNASampler(seed): 0.444 Carnac(20): 0.343 Positive Predictive Value RNASampler(seed): 0.768 Carnac(20): 0.965 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.714 RNASampler(seed): 0.680 Sensitivity Afold: 0.668 RNASampler(seed): 0.550 Positive Predictive Value Afold: 0.766 RNASampler(seed): 0.845 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.43573297697e-08	17 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.673 RNAsubopt: 0.636 Sensitivity RNASampler(seed): 0.535 RNAsubopt: 0.595 Positive Predictive Value RNASampler(seed): 0.851 RNAsubopt: 0.685 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	7 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.702 RNASampler(seed): 0.613 Sensitivity Cylofold: 0.620 RNASampler(seed): 0.460 Positive Predictive Value Cylofold: 0.800 RNASampler(seed): 0.821 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.680 RNASampler(seed): 0.673 Sensitivity McQFold: 0.619 RNASampler(seed): 0.535 Positive Predictive Value McQFold: 0.751 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 7.5822376376e-06	17 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 RNAalifold(seed): 0.646 Sensitivity RNASampler(seed): 0.535 RNAalifold(seed): 0.483 Positive Predictive Value RNASampler(seed): 0.851 RNAalifold(seed): 0.868 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.701 RNASampler(seed): 0.673 Sensitivity Pknots: 0.668 RNASampler(seed): 0.535 Positive Predictive Value Pknots: 0.739 RNASampler(seed): 0.851 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.87234834547e-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: 1.50834591464e-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	? RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RSpredict(20): 0.507 Sensitivity RNASampler(seed): 0.444 RSpredict(20): 0.464 Positive Predictive Value RNASampler(seed): 0.768 RSpredict(20): 0.558 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Mastr(20): 0.562 Sensitivity RNASampler(seed): 0.444 Mastr(20): 0.351 Positive Predictive Value RNASampler(seed): 0.768 Mastr(20): 0.903 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.673 Vsfold4: 0.595 Sensitivity RNASampler(seed): 0.535 Vsfold4: 0.521 Positive Predictive Value RNASampler(seed): 0.851 Vsfold4: 0.686 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.295 RNASampler(seed): 0.198 Sensitivity RNASLOpt: 0.283 RNASampler(seed): 0.151 Positive Predictive Value RNASLOpt: 0.313 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? 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	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.471 RNAwolf: 0.416 Sensitivity RNASampler(seed): 0.341 RNAwolf: 0.403 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Murlet(seed): 0.564 Sensitivity RNASampler(seed): 0.535 Murlet(seed): 0.385 Positive Predictive Value RNASampler(seed): 0.851 Murlet(seed): 0.832 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.673 MCFold: 0.595 Sensitivity RNASampler(seed): 0.535 MCFold: 0.619 Positive Predictive Value RNASampler(seed): 0.851 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.673 Vsfold5: 0.621 Sensitivity RNASampler(seed): 0.535 Vsfold5: 0.559 Positive Predictive Value RNASampler(seed): 0.851 Vsfold5: 0.695 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.753 RDfolder: 0.674 Sensitivity RNASampler(seed): 0.603 RDfolder: 0.552 Positive Predictive Value RNASampler(seed): 0.946 RDfolder: 0.831 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 RSpredict(seed): 0.555 Sensitivity RNASampler(seed): 0.535 RSpredict(seed): 0.390 Positive Predictive Value RNASampler(seed): 0.851 RSpredict(seed): 0.795 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 PPfold(seed): 0.169 Sensitivity RNASampler(seed): 0.341 PPfold(seed): 0.054 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.198 NanoFolder: 0.171 Sensitivity RNASampler(seed): 0.151 NanoFolder: 0.208 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Mastr(seed): 0.483 Sensitivity RNASampler(seed): 0.535 Mastr(seed): 0.261 Positive Predictive Value RNASampler(seed): 0.851 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-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	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.588 RNASampler(seed): 0.564 Sensitivity Multilign(seed): 0.483 RNASampler(seed): 0.405 Positive Predictive Value Multilign(seed): 0.727 RNASampler(seed): 0.797 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 RNASampler(seed): 0.198 Sensitivity PETfold_pre2.0(seed): 0.396 RNASampler(seed): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.656 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 RNASampler(seed): 0.581 Sensitivity TurboFold(20): 0.488 RNASampler(seed): 0.426 Positive Predictive Value TurboFold(20): 0.700 RNASampler(seed): 0.797 Number of pairs reference - predicted secondary structure: 4 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 PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.310 PETfold_pre2.0(20): 0.193 Sensitivity RNASampler(seed): 0.242 PETfold_pre2.0(20): 0.152 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.504 TurboFold(seed): 0.480 Sensitivity RNASampler(seed): 0.369 TurboFold(seed): 0.423 Positive Predictive Value RNASampler(seed): 0.696 TurboFold(seed): 0.553 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.581 PPfold(20): 0.569 Sensitivity RNASampler(seed): 0.426 PPfold(20): 0.426 Positive Predictive Value RNASampler(seed): 0.797 PPfold(20): 0.764 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Carnac(seed): 0.379 Sensitivity RNASampler(seed): 0.535 Carnac(seed): 0.145 Positive Predictive Value RNASampler(seed): 0.851 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08
CRWrnafold	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	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	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 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	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	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: 3.85233844192e-08	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 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	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: 8.68922211961e-08	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: 4.48494289621e-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: 3.56938820447e-08	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	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: 0.000524630860266	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: 8.62431444312e-06	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: 5.19332990918e-08	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: 2.28033735003e-07	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: 5.6410608252e-08	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: 3.85233844192e-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	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: 0.000120940900885	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	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	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: 3.27388928538e-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: 0.0360075305827	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: 0.00683149332667	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: 0.125446474224	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 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: 4.83792096436e-08	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: 0.00139331462707	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		? 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	? 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	+ 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: 1.61106400375e-07	? 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 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	? 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 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: 3.56938820447e-08	+ 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 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: 5.19332990918e-08	? 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 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 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: 1.70887622364e-08	? 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	? CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): N/A CRWrnafold: N/A Sensitivity CMfinder(seed): N/A CRWrnafold: N/A Positive Predictive Value CMfinder(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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
RSpredict(20)	27 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 RSpredict(20): 0.547 Sensitivity MXScarna(seed): 0.556 RSpredict(20): 0.428 Positive Predictive Value MXScarna(seed): 0.805 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.597 RSpredict(20): 0.543 Sensitivity CentroidFold: 0.506 RSpredict(20): 0.425 Positive Predictive Value CentroidFold: 0.707 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RSpredict(20): 0.543 Sensitivity CentroidAlifold(20): 0.520 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.892 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(20): 0.547 Sensitivity RNAalifold(20): 0.491 RSpredict(20): 0.428 Positive Predictive Value RNAalifold(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.640 RSpredict(20): 0.547 Sensitivity RNASampler(20): 0.489 RSpredict(20): 0.428 Positive Predictive Value RNASampler(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	27 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.594 RSpredict(20): 0.547 Sensitivity Sfold: 0.500 RSpredict(20): 0.428 Positive Predictive Value Sfold: 0.710 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.634 RSpredict(20): 0.547 Sensitivity MXScarna(20): 0.530 RSpredict(20): 0.428 Positive Predictive Value MXScarna(20): 0.761 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.556 RSpredict(20): 0.547 Sensitivity Contrafold: 0.495 RSpredict(20): 0.428 Positive Predictive Value Contrafold: 0.630 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.69838533668e-06	18 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.610 RSpredict(20): 0.524 Sensitivity Fold: 0.542 RSpredict(20): 0.403 Positive Predictive Value Fold: 0.689 RSpredict(20): 0.684 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	27 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.581 RSpredict(20): 0.547 Sensitivity HotKnots: 0.521 RSpredict(20): 0.428 Positive Predictive Value HotKnots: 0.653 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RSpredict(20): 0.494 Sensitivity CentroidHomfold‑LAST: 0.524 RSpredict(20): 0.376 Positive Predictive Value CentroidHomfold‑LAST: 0.822 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.571 RSpredict(20): 0.489 Sensitivity IPknot: 0.463 RSpredict(20): 0.367 Positive Predictive Value IPknot: 0.710 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.588 RSpredict(20): 0.543 Sensitivity MaxExpect: 0.516 RSpredict(20): 0.425 Positive Predictive Value MaxExpect: 0.675 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.589 RSpredict(20): 0.547 Sensitivity UNAFold: 0.519 RSpredict(20): 0.428 Positive Predictive Value UNAFold: 0.673 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.579 RSpredict(20): 0.352 Sensitivity ContextFold: 0.443 RSpredict(20): 0.251 Positive Predictive Value ContextFold: 0.763 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	27 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.586 RSpredict(20): 0.547 Sensitivity RNAshapes: 0.516 RSpredict(20): 0.428 Positive Predictive Value RNAshapes: 0.670 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.570 RSpredict(20): 0.547 Sensitivity RNAfold: 0.509 RSpredict(20): 0.428 Positive Predictive Value RNAfold: 0.643 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 7.27211512036e-08	27 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.581 RSpredict(20): 0.547 Sensitivity PknotsRG: 0.521 RSpredict(20): 0.428 Positive Predictive Value PknotsRG: 0.651 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.48494289621e-08	26 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 RSpredict(20): 0.543 Sensitivity CentroidAlifold(seed): 0.430 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.923 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.586 RSpredict(20): 0.524 Sensitivity ProbKnot: 0.529 RSpredict(20): 0.403 Positive Predictive Value ProbKnot: 0.653 RSpredict(20): 0.684 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	27 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.582 RSpredict(20): 0.547 Sensitivity Murlet(20): 0.425 RSpredict(20): 0.428 Positive Predictive Value Murlet(20): 0.800 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.586 RSpredict(20): 0.547 Sensitivity Carnac(20): 0.377 RSpredict(20): 0.428 Positive Predictive Value Carnac(20): 0.916 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.551 Afold: 0.521 Sensitivity RSpredict(20): 0.456 Afold: 0.479 Positive Predictive Value RSpredict(20): 0.670 Afold: 0.571 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 4.98606912064e-08	27 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.564 RSpredict(20): 0.547 Sensitivity RNAsubopt: 0.507 RSpredict(20): 0.428 Positive Predictive Value RNAsubopt: 0.631 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.64876692942e-07	14 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.608 RSpredict(20): 0.585 Sensitivity Cylofold: 0.523 RSpredict(20): 0.456 Positive Predictive Value Cylofold: 0.712 RSpredict(20): 0.757 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	27 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.547 McQFold: 0.536 Sensitivity RSpredict(20): 0.428 McQFold: 0.468 Positive Predictive Value RSpredict(20): 0.702 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000204094570084	18 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 RSpredict(20): 0.480 Sensitivity RNAalifold(seed): 0.356 RSpredict(20): 0.363 Positive Predictive Value RNAalifold(seed): 0.923 RSpredict(20): 0.640 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	26 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.549 Pknots: 0.547 Sensitivity RSpredict(20): 0.428 Pknots: 0.501 Positive Predictive Value RSpredict(20): 0.712 Pknots: 0.604 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0484227593148	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: 1.25253056981e-08	8 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 RSpredict(20): 0.507 Sensitivity RNASampler(seed): 0.444 RSpredict(20): 0.464 Positive Predictive Value RNASampler(seed): 0.768 RSpredict(20): 0.558 Number of pairs reference - predicted secondary structure: 8 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		+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.547 Mastr(20): 0.527 Sensitivity RSpredict(20): 0.428 Mastr(20): 0.348 Positive Predictive Value RSpredict(20): 0.702 Mastr(20): 0.803 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.54918844895e-07	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.547 Vsfold4: 0.458 Sensitivity RSpredict(20): 0.428 Vsfold4: 0.388 Positive Predictive Value RSpredict(20): 0.702 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.467 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.383 RSpredict(20): 0.251 Positive Predictive Value RNASLOpt: 0.577 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.521 RSpredict(20): 0.487 Sensitivity Multilign(20): 0.428 RSpredict(20): 0.355 Positive Predictive Value Multilign(20): 0.643 RSpredict(20): 0.674 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.07620071341e-09	? RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.489 RNAwolf: 0.364 Sensitivity RSpredict(20): 0.367 RNAwolf: 0.333 Positive Predictive Value RSpredict(20): 0.660 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.491 RSpredict(20): 0.468 Sensitivity Murlet(seed): 0.269 RSpredict(20): 0.347 Positive Predictive Value Murlet(seed): 0.901 RSpredict(20): 0.638 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.44854136456e-07	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.580 MCFold: 0.421 Sensitivity RSpredict(20): 0.468 MCFold: 0.445 Positive Predictive Value RSpredict(20): 0.724 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.547 Vsfold5: 0.423 Sensitivity RSpredict(20): 0.428 Vsfold5: 0.363 Positive Predictive Value RSpredict(20): 0.702 Vsfold5: 0.499 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.623 RDfolder: 0.529 Sensitivity RSpredict(20): 0.472 RDfolder: 0.431 Positive Predictive Value RSpredict(20): 0.829 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.547 RSpredict(seed): 0.249 Sensitivity RSpredict(20): 0.428 RSpredict(seed): 0.110 Positive Predictive Value RSpredict(20): 0.702 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 PPfold(seed): 0.026 Sensitivity RSpredict(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value RSpredict(20): 0.660 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.337 NanoFolder: 0.316 Sensitivity RSpredict(20): 0.243 NanoFolder: 0.324 Positive Predictive Value RSpredict(20): 0.474 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.547 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.428 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.702 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-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	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.678 RSpredict(20): 0.583 Sensitivity Multilign(seed): 0.543 RSpredict(20): 0.449 Positive Predictive Value Multilign(seed): 0.852 RSpredict(20): 0.765 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(seed): 0.557 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.620 RSpredict(20): 0.494 Sensitivity TurboFold(20): 0.500 RSpredict(20): 0.376 Positive Predictive Value TurboFold(20): 0.775 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 RSpredict(20): 0.484 Sensitivity TurboFold(seed): 0.490 RSpredict(20): 0.373 Positive Predictive Value TurboFold(seed): 0.729 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(20): 0.494 Sensitivity PPfold(20): 0.514 RSpredict(20): 0.376 Positive Predictive Value PPfold(20): 0.861 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.514 Carnac(seed): 0.197 Sensitivity RSpredict(20): 0.394 Carnac(seed): 0.039 Positive Predictive Value RSpredict(20): 0.677 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
Mastr(20)	27 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.668 Mastr(20): 0.527 Sensitivity MXScarna(seed): 0.556 Mastr(20): 0.348 Positive Predictive Value MXScarna(seed): 0.805 Mastr(20): 0.803 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.597 Mastr(20): 0.521 Sensitivity CentroidFold: 0.506 Mastr(20): 0.342 Positive Predictive Value CentroidFold: 0.707 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Mastr(20): 0.521 Sensitivity CentroidAlifold(20): 0.520 Mastr(20): 0.342 Positive Predictive Value CentroidAlifold(20): 0.892 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.644 Mastr(20): 0.525 Sensitivity RNAalifold(20): 0.491 Mastr(20): 0.346 Positive Predictive Value RNAalifold(20): 0.849 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(20): 0.525 Sensitivity RNASampler(20): 0.477 Mastr(20): 0.346 Positive Predictive Value RNASampler(20): 0.844 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.590 Mastr(20): 0.525 Sensitivity Sfold: 0.493 Mastr(20): 0.346 Positive Predictive Value Sfold: 0.709 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.628 Mastr(20): 0.525 Sensitivity MXScarna(20): 0.523 Mastr(20): 0.346 Positive Predictive Value MXScarna(20): 0.757 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.544 Mastr(20): 0.525 Sensitivity Contrafold: 0.481 Mastr(20): 0.346 Positive Predictive Value Contrafold: 0.619 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.72695708134e-06	18 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.610 Mastr(20): 0.491 Sensitivity Fold: 0.542 Mastr(20): 0.300 Positive Predictive Value Fold: 0.689 Mastr(20): 0.808 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	28 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.577 Mastr(20): 0.525 Sensitivity HotKnots: 0.514 Mastr(20): 0.346 Positive Predictive Value HotKnots: 0.652 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Mastr(20): 0.592 Sensitivity CentroidHomfold‑LAST: 0.524 Mastr(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.571 Mastr(20): 0.567 Sensitivity IPknot: 0.463 Mastr(20): 0.389 Positive Predictive Value IPknot: 0.710 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.588 Mastr(20): 0.521 Sensitivity MaxExpect: 0.516 Mastr(20): 0.342 Positive Predictive Value MaxExpect: 0.675 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.585 Mastr(20): 0.525 Sensitivity UNAFold: 0.512 Mastr(20): 0.346 Positive Predictive Value UNAFold: 0.672 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.579 Mastr(20): 0.488 Sensitivity ContextFold: 0.443 Mastr(20): 0.305 Positive Predictive Value ContextFold: 0.763 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.577 Mastr(20): 0.525 Sensitivity RNAshapes: 0.506 Mastr(20): 0.346 Positive Predictive Value RNAshapes: 0.664 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.567 Mastr(20): 0.525 Sensitivity RNAfold: 0.503 Mastr(20): 0.346 Positive Predictive Value RNAfold: 0.644 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	28 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.579 Mastr(20): 0.525 Sensitivity PknotsRG: 0.516 Mastr(20): 0.346 Positive Predictive Value PknotsRG: 0.653 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Mastr(20): 0.521 Sensitivity CentroidAlifold(seed): 0.430 Mastr(20): 0.342 Positive Predictive Value CentroidAlifold(seed): 0.923 Mastr(20): 0.799 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.586 Mastr(20): 0.491 Sensitivity ProbKnot: 0.529 Mastr(20): 0.300 Positive Predictive Value ProbKnot: 0.653 Mastr(20): 0.808 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	28 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.582 Mastr(20): 0.525 Sensitivity Murlet(20): 0.423 Mastr(20): 0.346 Positive Predictive Value Murlet(20): 0.804 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.582 Mastr(20): 0.525 Sensitivity Carnac(20): 0.371 Mastr(20): 0.346 Positive Predictive Value Carnac(20): 0.915 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.523 Afold: 0.518 Sensitivity Mastr(20): 0.343 Afold: 0.469 Positive Predictive Value Mastr(20): 0.800 Afold: 0.576 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.0190329081063	28 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.550 Mastr(20): 0.525 Sensitivity RNAsubopt: 0.492 Mastr(20): 0.346 Positive Predictive Value RNAsubopt: 0.619 Mastr(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.6710542315e-07	14 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.608 Mastr(20): 0.565 Sensitivity Cylofold: 0.523 Mastr(20): 0.375 Positive Predictive Value Cylofold: 0.712 Mastr(20): 0.856 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.35270341049e-08	28 Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.525 McQFold: 0.524 Sensitivity Mastr(20): 0.346 McQFold: 0.454 Positive Predictive Value Mastr(20): 0.800 McQFold: 0.609 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.215158657328	18 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Mastr(20): 0.415 Sensitivity RNAalifold(seed): 0.356 Mastr(20): 0.221 Positive Predictive Value RNAalifold(seed): 0.923 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	27 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.560 Pknots: 0.530 Sensitivity Mastr(20): 0.395 Pknots: 0.483 Positive Predictive Value Mastr(20): 0.800 Pknots: 0.589 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.01557756351e-08	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: 2.30549897711e-08	8 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.582 Mastr(20): 0.562 Sensitivity RNASampler(seed): 0.444 Mastr(20): 0.351 Positive Predictive Value RNASampler(seed): 0.768 Mastr(20): 0.903 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	27 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.547 Mastr(20): 0.527 Sensitivity RSpredict(20): 0.428 Mastr(20): 0.348 Positive Predictive Value RSpredict(20): 0.702 Mastr(20): 0.803 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.54918844895e-07		+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold4: 0.450 Sensitivity Mastr(20): 0.346 Vsfold4: 0.379 Positive Predictive Value Mastr(20): 0.800 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.488 RNASLOpt: 0.467 Sensitivity Mastr(20): 0.305 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.785 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.572 Multilign(20): 0.521 Sensitivity Mastr(20): 0.386 Multilign(20): 0.428 Positive Predictive Value Mastr(20): 0.853 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.87872347734e-08	? Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.567 RNAwolf: 0.364 Sensitivity Mastr(20): 0.389 RNAwolf: 0.333 Positive Predictive Value Mastr(20): 0.833 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.491 Mastr(20): 0.460 Sensitivity Murlet(seed): 0.269 Mastr(20): 0.272 Positive Predictive Value Murlet(seed): 0.901 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.591 MCFold: 0.421 Sensitivity Mastr(20): 0.417 MCFold: 0.445 Positive Predictive Value Mastr(20): 0.844 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold5: 0.406 Sensitivity Mastr(20): 0.346 Vsfold5: 0.347 Positive Predictive Value Mastr(20): 0.800 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.655 RDfolder: 0.529 Sensitivity Mastr(20): 0.503 RDfolder: 0.431 Positive Predictive Value Mastr(20): 0.858 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.527 RSpredict(seed): 0.249 Sensitivity Mastr(20): 0.348 RSpredict(seed): 0.110 Positive Predictive Value Mastr(20): 0.803 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.567 PPfold(seed): 0.026 Sensitivity Mastr(20): 0.389 PPfold(seed): 0.004 Positive Predictive Value Mastr(20): 0.833 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.499 NanoFolder: 0.316 Sensitivity Mastr(20): 0.324 NanoFolder: 0.324 Positive Predictive Value Mastr(20): 0.774 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.525 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.346 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.800 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-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	? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Mastr(20): 0.611 Sensitivity Multilign(seed): 0.543 Mastr(20): 0.471 Positive Predictive Value Multilign(seed): 0.852 Mastr(20): 0.802 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(seed): 0.557 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Mastr(20): 0.592 Sensitivity TurboFold(20): 0.500 Mastr(20): 0.417 Positive Predictive Value TurboFold(20): 0.775 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): 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): 0.625 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Mastr(20): 0.572 Sensitivity TurboFold(seed): 0.490 Mastr(20): 0.399 Positive Predictive Value TurboFold(seed): 0.729 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(20): 0.592 Sensitivity PPfold(20): 0.514 Mastr(20): 0.417 Positive Predictive Value PPfold(20): 0.861 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.526 Carnac(seed): 0.197 Sensitivity Mastr(20): 0.357 Carnac(seed): 0.039 Positive Predictive Value Mastr(20): 0.780 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08
Vsfold4	44 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.673 Vsfold4: 0.517 Sensitivity MXScarna(seed): 0.562 Vsfold4: 0.445 Positive Predictive Value MXScarna(seed): 0.809 Vsfold4: 0.605 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.676 Vsfold4: 0.563 Sensitivity CentroidFold: 0.591 Vsfold4: 0.484 Positive Predictive Value CentroidFold: 0.777 Vsfold4: 0.661 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Vsfold4: 0.452 Sensitivity CentroidAlifold(20): 0.520 Vsfold4: 0.382 Positive Predictive Value CentroidAlifold(20): 0.892 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.644 Vsfold4: 0.450 Sensitivity RNAalifold(20): 0.491 Vsfold4: 0.379 Positive Predictive Value RNAalifold(20): 0.849 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.634 Vsfold4: 0.450 Sensitivity RNASampler(20): 0.477 Vsfold4: 0.379 Positive Predictive Value RNASampler(20): 0.844 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	118 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.669 Vsfold4: 0.562 Sensitivity Sfold: 0.581 Vsfold4: 0.481 Positive Predictive Value Sfold: 0.775 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.628 Vsfold4: 0.450 Sensitivity MXScarna(20): 0.523 Vsfold4: 0.379 Positive Predictive Value MXScarna(20): 0.757 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.660 Vsfold4: 0.562 Sensitivity Contrafold: 0.592 Vsfold4: 0.481 Positive Predictive Value Contrafold: 0.740 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.679 Vsfold4: 0.571 Sensitivity Fold: 0.618 Vsfold4: 0.494 Positive Predictive Value Fold: 0.751 Vsfold4: 0.666 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.662 Vsfold4: 0.562 Sensitivity HotKnots: 0.600 Vsfold4: 0.481 Positive Predictive Value HotKnots: 0.736 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.668 Vsfold4: 0.548 Sensitivity CentroidHomfold‑LAST: 0.515 Vsfold4: 0.462 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Vsfold4: 0.658 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.675 Vsfold4: 0.537 Sensitivity IPknot: 0.573 Vsfold4: 0.458 Positive Predictive Value IPknot: 0.801 Vsfold4: 0.639 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.653 Vsfold4: 0.560 Sensitivity MaxExpect: 0.587 Vsfold4: 0.480 Positive Predictive Value MaxExpect: 0.731 Vsfold4: 0.657 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.664 Vsfold4: 0.562 Sensitivity UNAFold: 0.595 Vsfold4: 0.481 Positive Predictive Value UNAFold: 0.747 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.705 Vsfold4: 0.537 Sensitivity ContextFold: 0.594 Vsfold4: 0.457 Positive Predictive Value ContextFold: 0.843 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.650 Vsfold4: 0.562 Sensitivity RNAshapes: 0.580 Vsfold4: 0.481 Positive Predictive Value RNAshapes: 0.733 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.651 Vsfold4: 0.562 Sensitivity RNAfold: 0.587 Vsfold4: 0.481 Positive Predictive Value RNAfold: 0.726 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.646 Vsfold4: 0.562 Sensitivity PknotsRG: 0.585 Vsfold4: 0.481 Positive Predictive Value PknotsRG: 0.718 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Vsfold4: 0.513 Sensitivity CentroidAlifold(seed): 0.419 Vsfold4: 0.441 Positive Predictive Value CentroidAlifold(seed): 0.878 Vsfold4: 0.601 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.646 Vsfold4: 0.547 Sensitivity ProbKnot: 0.597 Vsfold4: 0.471 Positive Predictive Value ProbKnot: 0.703 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.582 Vsfold4: 0.450 Sensitivity Murlet(20): 0.423 Vsfold4: 0.379 Positive Predictive Value Murlet(20): 0.804 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.582 Vsfold4: 0.450 Sensitivity Carnac(20): 0.371 Vsfold4: 0.379 Positive Predictive Value Carnac(20): 0.915 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	92 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.647 Vsfold4: 0.572 Sensitivity Afold: 0.595 Vsfold4: 0.494 Positive Predictive Value Afold: 0.709 Vsfold4: 0.670 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.635 Vsfold4: 0.562 Sensitivity RNAsubopt: 0.574 Vsfold4: 0.481 Positive Predictive Value RNAsubopt: 0.708 Vsfold4: 0.664 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.648 Vsfold4: 0.585 Sensitivity Cylofold: 0.559 Vsfold4: 0.499 Positive Predictive Value Cylofold: 0.758 Vsfold4: 0.694 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.620 Vsfold4: 0.560 Sensitivity McQFold: 0.540 Vsfold4: 0.479 Positive Predictive Value McQFold: 0.716 Vsfold4: 0.661 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.593 Vsfold4: 0.498 Sensitivity RNAalifold(seed): 0.397 Vsfold4: 0.432 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	116 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.634 Vsfold4: 0.584 Sensitivity Pknots: 0.575 Vsfold4: 0.497 Positive Predictive Value Pknots: 0.706 Vsfold4: 0.694 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	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: 4.83792096436e-08	17 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.673 Vsfold4: 0.595 Sensitivity RNASampler(seed): 0.535 Vsfold4: 0.521 Positive Predictive Value RNASampler(seed): 0.851 Vsfold4: 0.686 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-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	27 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.547 Vsfold4: 0.458 Sensitivity RSpredict(20): 0.428 Vsfold4: 0.388 Positive Predictive Value RSpredict(20): 0.702 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold4: 0.450 Sensitivity Mastr(20): 0.346 Vsfold4: 0.379 Positive Predictive Value Mastr(20): 0.800 Vsfold4: 0.541 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08		- RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.591 Vsfold4: 0.537 Sensitivity RNASLOpt: 0.498 Vsfold4: 0.457 Positive Predictive Value RNASLOpt: 0.709 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.521 Vsfold4: 0.412 Sensitivity Multilign(20): 0.428 Vsfold4: 0.340 Positive Predictive Value Multilign(20): 0.643 Vsfold4: 0.509 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.537 RNAwolf: 0.512 Sensitivity Vsfold4: 0.458 RNAwolf: 0.479 Positive Predictive Value Vsfold4: 0.639 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.48494289621e-08	= Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.539 Murlet(seed): 0.539 Sensitivity Vsfold4: 0.460 Murlet(seed): 0.337 Positive Predictive Value Vsfold4: 0.639 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.554240997957	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.593 MCFold: 0.577 Sensitivity Vsfold4: 0.507 MCFold: 0.597 Positive Predictive Value Vsfold4: 0.701 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.561 Vsfold5: 0.528 Sensitivity Vsfold4: 0.480 Vsfold5: 0.458 Positive Predictive Value Vsfold4: 0.662 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.655 RDfolder: 0.596 Sensitivity Vsfold4: 0.559 RDfolder: 0.495 Positive Predictive Value Vsfold4: 0.777 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.517 RSpredict(seed): 0.314 Sensitivity Vsfold4: 0.445 RSpredict(seed): 0.161 Positive Predictive Value Vsfold4: 0.605 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.454 PPfold(seed): 0.102 Sensitivity Vsfold4: 0.367 PPfold(seed): 0.020 Positive Predictive Value Vsfold4: 0.570 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.528 NanoFolder: 0.490 Sensitivity Vsfold4: 0.451 NanoFolder: 0.495 Positive Predictive Value Vsfold4: 0.627 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.509 Mastr(seed): 0.258 Sensitivity Vsfold4: 0.437 Mastr(seed): 0.075 Positive Predictive Value Vsfold4: 0.599 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.593 Vsfold4: 0.445 Sensitivity Multilign(seed): 0.475 Vsfold4: 0.367 Positive Predictive Value Multilign(seed): 0.750 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold4: 0.437 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold4: 0.350 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold4: 0.553 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.620 Vsfold4: 0.474 Sensitivity TurboFold(20): 0.500 Vsfold4: 0.390 Positive Predictive Value TurboFold(20): 0.775 Vsfold4: 0.585 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold4: 0.401 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold4: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold4: 0.505 Number of pairs reference - predicted secondary structure: 5 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	? PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.663 Vsfold4: 0.474 Sensitivity PPfold(20): 0.514 Vsfold4: 0.390 Positive Predictive Value PPfold(20): 0.861 Vsfold4: 0.585 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.531 Carnac(seed): 0.260 Sensitivity Vsfold4: 0.453 Carnac(seed): 0.068 Positive Predictive Value Vsfold4: 0.629 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	8 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.586 RNASLOpt: 0.474 Sensitivity MXScarna(seed): 0.457 RNASLOpt: 0.374 Positive Predictive Value MXScarna(seed): 0.758 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	30 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.654 RNASLOpt: 0.591 Sensitivity CentroidFold: 0.556 RNASLOpt: 0.498 Positive Predictive Value CentroidFold: 0.775 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.650 RNASLOpt: 0.467 Sensitivity CentroidAlifold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.898 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.553 RNASLOpt: 0.467 Sensitivity RNAalifold(20): 0.407 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.756 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.569 RNASLOpt: 0.467 Sensitivity RNASampler(20): 0.419 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.629 RNASLOpt: 0.591 Sensitivity Sfold: 0.536 RNASLOpt: 0.498 Positive Predictive Value Sfold: 0.744 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.501 RNASLOpt: 0.467 Sensitivity MXScarna(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.632 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.649 RNASLOpt: 0.591 Sensitivity Contrafold: 0.568 RNASLOpt: 0.498 Positive Predictive Value Contrafold: 0.749 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.609 RNASLOpt: 0.591 Sensitivity Fold: 0.543 RNASLOpt: 0.498 Positive Predictive Value Fold: 0.690 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.1569883686e-08	30 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.638 RNASLOpt: 0.591 Sensitivity HotKnots: 0.579 RNASLOpt: 0.498 Positive Predictive Value HotKnots: 0.709 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNASLOpt: 0.581 Sensitivity CentroidHomfold‑LAST: 0.502 RNASLOpt: 0.488 Positive Predictive Value CentroidHomfold‑LAST: 0.836 RNASLOpt: 0.699 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.665 RNASLOpt: 0.591 Sensitivity IPknot: 0.568 RNASLOpt: 0.498 Positive Predictive Value IPknot: 0.785 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.608 RNASLOpt: 0.591 Sensitivity MaxExpect: 0.536 RNASLOpt: 0.498 Positive Predictive Value MaxExpect: 0.696 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.18450348589e-07	30 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.600 RNASLOpt: 0.591 Sensitivity UNAFold: 0.538 RNASLOpt: 0.498 Positive Predictive Value UNAFold: 0.676 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.00151316827629	30 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.705 RNASLOpt: 0.591 Sensitivity ContextFold: 0.594 RNASLOpt: 0.498 Positive Predictive Value ContextFold: 0.843 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.617 RNASLOpt: 0.591 Sensitivity RNAshapes: 0.548 RNASLOpt: 0.498 Positive Predictive Value RNAshapes: 0.702 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.62644058675e-08	30 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.624 RNASLOpt: 0.591 Sensitivity RNAfold: 0.554 RNASLOpt: 0.498 Positive Predictive Value RNAfold: 0.709 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.637 RNASLOpt: 0.591 Sensitivity PknotsRG: 0.574 RNASLOpt: 0.498 Positive Predictive Value PknotsRG: 0.713 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.542 RNASLOpt: 0.474 Sensitivity CentroidAlifold(seed): 0.299 RNASLOpt: 0.374 Positive Predictive Value CentroidAlifold(seed): 0.987 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	30 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.611 RNASLOpt: 0.591 Sensitivity ProbKnot: 0.558 RNASLOpt: 0.498 Positive Predictive Value ProbKnot: 0.676 RNASLOpt: 0.709 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.25365426827e-07	5 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.496 RNASLOpt: 0.467 Sensitivity Murlet(20): 0.353 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.702 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.476 RNASLOpt: 0.467 Sensitivity Carnac(20): 0.281 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.810 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	18 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.677 RNASLOpt: 0.646 Sensitivity Afold: 0.624 RNASLOpt: 0.572 Positive Predictive Value Afold: 0.740 RNASLOpt: 0.736 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	30 RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.591 RNAsubopt: 0.584 Sensitivity RNASLOpt: 0.498 RNAsubopt: 0.525 Positive Predictive Value RNASLOpt: 0.709 RNAsubopt: 0.658 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.000579628272742	23 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.580 Cylofold: 0.578 Sensitivity RNASLOpt: 0.477 Cylofold: 0.494 Positive Predictive Value RNASLOpt: 0.713 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.605145451624	29 RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.581 McQFold: 0.578 Sensitivity RNASLOpt: 0.488 McQFold: 0.505 Positive Predictive Value RNASLOpt: 0.699 McQFold: 0.670 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0146580879528	5 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNASLOpt: 0.390 Sensitivity RNAalifold(seed): 0.293 RNASLOpt: 0.323 Positive Predictive Value RNAalifold(seed): 0.765 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.591 Pknots: 0.547 Sensitivity RNASLOpt: 0.498 Pknots: 0.497 Positive Predictive Value RNASLOpt: 0.709 Pknots: 0.611 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.48494289621e-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: 2.57237423209e-08	2 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.295 RNASampler(seed): 0.198 Sensitivity RNASLOpt: 0.283 RNASampler(seed): 0.151 Positive Predictive Value RNASLOpt: 0.313 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	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: 1.61106400375e-07	5 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.467 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.383 RSpredict(20): 0.251 Positive Predictive Value RNASLOpt: 0.577 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.488 RNASLOpt: 0.467 Sensitivity Mastr(20): 0.305 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.785 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.591 Vsfold4: 0.537 Sensitivity RNASLOpt: 0.498 Vsfold4: 0.457 Positive Predictive Value RNASLOpt: 0.709 Vsfold4: 0.640 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08		? Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.474 RNASLOpt: 0.467 Sensitivity Multilign(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value Multilign(20): 0.568 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.591 RNAwolf: 0.488 Sensitivity RNASLOpt: 0.498 RNAwolf: 0.457 Positive Predictive Value RNASLOpt: 0.709 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.425 RNASLOpt: 0.390 Sensitivity Murlet(seed): 0.248 RNASLOpt: 0.323 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.621 MCFold: 0.596 Sensitivity RNASLOpt: 0.535 MCFold: 0.626 Positive Predictive Value RNASLOpt: 0.727 MCFold: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.586 Vsfold5: 0.468 Sensitivity RNASLOpt: 0.492 Vsfold5: 0.408 Positive Predictive Value RNASLOpt: 0.704 Vsfold5: 0.545 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.571 RDfolder: 0.481 Sensitivity RNASLOpt: 0.462 RDfolder: 0.379 Positive Predictive Value RNASLOpt: 0.718 RDfolder: 0.623 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	? RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RSpredict(seed): 0.110 Sensitivity RNASLOpt: 0.374 RSpredict(seed): 0.047 Positive Predictive Value RNASLOpt: 0.609 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 PPfold(seed): 0.121 Sensitivity RNASLOpt: 0.374 PPfold(seed): 0.028 Positive Predictive Value RNASLOpt: 0.609 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.591 NanoFolder: 0.490 Sensitivity RNASLOpt: 0.500 NanoFolder: 0.495 Positive Predictive Value RNASLOpt: 0.705 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	? RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.374 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.609 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.403 RNASLOpt: 0.332 Sensitivity Multilign(seed): 0.306 RNASLOpt: 0.242 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNASLOpt: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 RNASLOpt: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.542 RNASLOpt: 0.467 Sensitivity TurboFold(20): 0.425 RNASLOpt: 0.383 Positive Predictive Value TurboFold(20): 0.696 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASLOpt: 0.467 Sensitivity PETfold_pre2.0(20): 0.497 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 TurboFold(seed): 0.460 Sensitivity RNASLOpt: 0.380 TurboFold(seed): 0.380 Positive Predictive Value RNASLOpt: 0.582 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.616 RNASLOpt: 0.467 Sensitivity PPfold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value PPfold(20): 0.806 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 Carnac(seed): 0.146 Sensitivity RNASLOpt: 0.380 Carnac(seed): 0.021 Positive Predictive Value RNASLOpt: 0.582 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
Multilign(20)	10 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.639 Multilign(20): 0.521 Sensitivity MXScarna(seed): 0.521 Multilign(20): 0.428 Positive Predictive Value MXScarna(seed): 0.790 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	10 CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.548 Multilign(20): 0.521 Sensitivity CentroidFold: 0.452 Multilign(20): 0.428 Positive Predictive Value CentroidFold: 0.673 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	10 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.657 Multilign(20): 0.521 Sensitivity CentroidAlifold(20): 0.476 Multilign(20): 0.428 Positive Predictive Value CentroidAlifold(20): 0.913 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.03233993685e-09	10 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.596 Multilign(20): 0.521 Sensitivity RNAalifold(20): 0.443 Multilign(20): 0.428 Positive Predictive Value RNAalifold(20): 0.808 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	10 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.626 Multilign(20): 0.521 Sensitivity RNASampler(20): 0.455 Multilign(20): 0.428 Positive Predictive Value RNASampler(20): 0.868 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	10 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.578 Multilign(20): 0.521 Sensitivity Sfold: 0.476 Multilign(20): 0.428 Positive Predictive Value Sfold: 0.709 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.21584974784e-08	10 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Multilign(20): 0.521 Sensitivity MXScarna(20): 0.518 Multilign(20): 0.428 Positive Predictive Value MXScarna(20): 0.761 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.9460272886e-09	10 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.528 Multilign(20): 0.521 Sensitivity Contrafold: 0.458 Multilign(20): 0.428 Positive Predictive Value Contrafold: 0.615 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000723083277971	10 Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.596 Multilign(20): 0.521 Sensitivity Fold: 0.524 Multilign(20): 0.428 Positive Predictive Value Fold: 0.685 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.95402773876e-08	10 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.599 Multilign(20): 0.521 Sensitivity HotKnots: 0.524 Multilign(20): 0.428 Positive Predictive Value HotKnots: 0.690 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.78774507289e-09	9 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Multilign(20): 0.574 Sensitivity CentroidHomfold‑LAST: 0.524 Multilign(20): 0.490 Positive Predictive Value CentroidHomfold‑LAST: 0.822 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.571 Multilign(20): 0.540 Sensitivity IPknot: 0.463 Multilign(20): 0.456 Positive Predictive Value IPknot: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.531 Multilign(20): 0.521 Sensitivity MaxExpect: 0.464 Multilign(20): 0.428 Positive Predictive Value MaxExpect: 0.616 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.08077114986e-06	10 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.557 Multilign(20): 0.521 Sensitivity UNAFold: 0.482 Multilign(20): 0.428 Positive Predictive Value UNAFold: 0.650 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	5 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.579 Multilign(20): 0.474 Sensitivity ContextFold: 0.443 Multilign(20): 0.401 Positive Predictive Value ContextFold: 0.763 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.633 Multilign(20): 0.521 Sensitivity RNAshapes: 0.548 Multilign(20): 0.428 Positive Predictive Value RNAshapes: 0.737 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	10 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.556 Multilign(20): 0.521 Sensitivity RNAfold: 0.482 Multilign(20): 0.428 Positive Predictive Value RNAfold: 0.648 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	10 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.592 Multilign(20): 0.521 Sensitivity PknotsRG: 0.521 Multilign(20): 0.428 Positive Predictive Value PknotsRG: 0.678 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	10 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.645 Multilign(20): 0.521 Sensitivity CentroidAlifold(seed): 0.449 Multilign(20): 0.428 Positive Predictive Value CentroidAlifold(seed): 0.931 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.35568223474e-09	10 ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.533 Multilign(20): 0.521 Sensitivity ProbKnot: 0.479 Multilign(20): 0.428 Positive Predictive Value ProbKnot: 0.600 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.4327622078e-07	10 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.557 Multilign(20): 0.521 Sensitivity Murlet(20): 0.404 Multilign(20): 0.428 Positive Predictive Value Murlet(20): 0.775 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.1398907247e-09	10 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.521 Carnac(20): 0.513 Sensitivity Multilign(20): 0.428 Carnac(20): 0.307 Positive Predictive Value Multilign(20): 0.643 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0111379505373	5 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.503 Multilign(20): 0.412 Sensitivity Afold: 0.459 Multilign(20): 0.338 Positive Predictive Value Afold: 0.557 Multilign(20): 0.510 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.569 Multilign(20): 0.521 Sensitivity RNAsubopt: 0.497 Multilign(20): 0.428 Positive Predictive Value RNAsubopt: 0.657 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	8 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.577 Multilign(20): 0.546 Sensitivity Cylofold: 0.494 Multilign(20): 0.429 Positive Predictive Value Cylofold: 0.684 Multilign(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.524 Multilign(20): 0.521 Sensitivity McQFold: 0.455 Multilign(20): 0.428 Positive Predictive Value McQFold: 0.611 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0977095104109	8 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.572 Multilign(20): 0.468 Sensitivity RNAalifold(seed): 0.355 Multilign(20): 0.378 Positive Predictive Value RNAalifold(seed): 0.927 Multilign(20): 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.521 Pknots: 0.507 Sensitivity Multilign(20): 0.428 Pknots: 0.452 Positive Predictive Value Multilign(20): 0.643 Pknots: 0.577 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.63256991408e-05	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	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	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	10 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.521 RSpredict(20): 0.487 Sensitivity Multilign(20): 0.428 RSpredict(20): 0.355 Positive Predictive Value Multilign(20): 0.643 RSpredict(20): 0.674 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.07620071341e-09	10 Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.572 Multilign(20): 0.521 Sensitivity Mastr(20): 0.386 Multilign(20): 0.428 Positive Predictive Value Mastr(20): 0.853 Multilign(20): 0.643 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.87872347734e-08	10 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.521 Vsfold4: 0.412 Sensitivity Multilign(20): 0.428 Vsfold4: 0.340 Positive Predictive Value Multilign(20): 0.643 Vsfold4: 0.509 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	5 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.474 RNASLOpt: 0.467 Sensitivity Multilign(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value Multilign(20): 0.568 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.540 RNAwolf: 0.364 Sensitivity Multilign(20): 0.456 RNAwolf: 0.333 Positive Predictive Value Multilign(20): 0.647 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.505 Multilign(20): 0.468 Sensitivity Murlet(seed): 0.279 Multilign(20): 0.378 Positive Predictive Value Murlet(seed): 0.921 Multilign(20): 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.526 MCFold: 0.461 Sensitivity Multilign(20): 0.434 MCFold: 0.472 Positive Predictive Value Multilign(20): 0.643 MCFold: 0.458 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): 0.521 Vsfold5: 0.402 Sensitivity Multilign(20): 0.428 Vsfold5: 0.349 Positive Predictive Value Multilign(20): 0.643 Vsfold5: 0.472 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.626 RDfolder: 0.478 Sensitivity Multilign(20): 0.517 RDfolder: 0.360 Positive Predictive Value Multilign(20): 0.766 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.521 RSpredict(seed): 0.304 Sensitivity Multilign(20): 0.428 RSpredict(seed): 0.142 Positive Predictive Value Multilign(20): 0.643 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	? Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.540 PPfold(seed): 0.026 Sensitivity Multilign(20): 0.456 PPfold(seed): 0.004 Positive Predictive Value Multilign(20): 0.647 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.490 NanoFolder: 0.316 Sensitivity Multilign(20): 0.419 NanoFolder: 0.324 Positive Predictive Value Multilign(20): 0.579 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.521 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.428 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.643 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.21563533328e-09	? 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	? 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	? PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(seed): 0.557 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Multilign(20): 0.574 Sensitivity TurboFold(20): 0.500 Multilign(20): 0.490 Positive Predictive Value TurboFold(20): 0.775 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(20): 0.497 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? 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	? PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.663 Multilign(20): 0.574 Sensitivity PPfold(20): 0.514 Multilign(20): 0.490 Positive Predictive Value PPfold(20): 0.861 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.511 Carnac(seed): 0.249 Sensitivity Multilign(20): 0.416 Carnac(seed): 0.062 Positive Predictive Value Multilign(20): 0.635 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
RNAwolf	11 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.624 RNAwolf: 0.414 Sensitivity MXScarna(seed): 0.493 RNAwolf: 0.375 Positive Predictive Value MXScarna(seed): 0.796 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.45096400029e-08	38 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.665 RNAwolf: 0.512 Sensitivity CentroidFold: 0.565 RNAwolf: 0.479 Positive Predictive Value CentroidFold: 0.789 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.691 RNAwolf: 0.364 Sensitivity CentroidAlifold(20): 0.515 RNAwolf: 0.333 Positive Predictive Value CentroidAlifold(20): 0.933 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.627 RNAwolf: 0.364 Sensitivity RNAalifold(20): 0.481 RNAwolf: 0.333 Positive Predictive Value RNAalifold(20): 0.823 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.637 RNAwolf: 0.364 Sensitivity RNASampler(20): 0.478 RNAwolf: 0.333 Positive Predictive Value RNASampler(20): 0.854 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.638 RNAwolf: 0.512 Sensitivity Sfold: 0.542 RNAwolf: 0.479 Positive Predictive Value Sfold: 0.758 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.586 RNAwolf: 0.364 Sensitivity MXScarna(20): 0.474 RNAwolf: 0.333 Positive Predictive Value MXScarna(20): 0.731 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.658 RNAwolf: 0.512 Sensitivity Contrafold: 0.576 RNAwolf: 0.479 Positive Predictive Value Contrafold: 0.759 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.611 RNAwolf: 0.512 Sensitivity Fold: 0.545 RNAwolf: 0.479 Positive Predictive Value Fold: 0.692 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.641 RNAwolf: 0.512 Sensitivity HotKnots: 0.577 RNAwolf: 0.479 Positive Predictive Value HotKnots: 0.719 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.670 RNAwolf: 0.502 Sensitivity CentroidHomfold‑LAST: 0.522 RNAwolf: 0.469 Positive Predictive Value CentroidHomfold‑LAST: 0.866 RNAwolf: 0.546 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.675 RNAwolf: 0.512 Sensitivity IPknot: 0.573 RNAwolf: 0.479 Positive Predictive Value IPknot: 0.801 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.613 RNAwolf: 0.512 Sensitivity MaxExpect: 0.541 RNAwolf: 0.479 Positive Predictive Value MaxExpect: 0.701 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.610 RNAwolf: 0.512 Sensitivity UNAFold: 0.543 RNAwolf: 0.479 Positive Predictive Value UNAFold: 0.693 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.705 RNAwolf: 0.488 Sensitivity ContextFold: 0.594 RNAwolf: 0.457 Positive Predictive Value ContextFold: 0.843 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.623 RNAwolf: 0.512 Sensitivity RNAshapes: 0.551 RNAwolf: 0.479 Positive Predictive Value RNAshapes: 0.711 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.628 RNAwolf: 0.512 Sensitivity RNAfold: 0.556 RNAwolf: 0.479 Positive Predictive Value RNAfold: 0.717 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.637 RNAwolf: 0.512 Sensitivity PknotsRG: 0.572 RNAwolf: 0.479 Positive Predictive Value PknotsRG: 0.716 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 RNAwolf: 0.414 Sensitivity CentroidAlifold(seed): 0.347 RNAwolf: 0.375 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.08932646657e-08	38 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.610 RNAwolf: 0.512 Sensitivity ProbKnot: 0.555 RNAwolf: 0.479 Positive Predictive Value ProbKnot: 0.679 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.581 RNAwolf: 0.364 Sensitivity Murlet(20): 0.433 RNAwolf: 0.333 Positive Predictive Value Murlet(20): 0.785 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.560 RNAwolf: 0.364 Sensitivity Carnac(20): 0.367 RNAwolf: 0.333 Positive Predictive Value Carnac(20): 0.861 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	24 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.670 RNAwolf: 0.595 Sensitivity Afold: 0.615 RNAwolf: 0.563 Positive Predictive Value Afold: 0.738 RNAwolf: 0.636 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.604 RNAwolf: 0.512 Sensitivity RNAsubopt: 0.538 RNAwolf: 0.479 Positive Predictive Value RNAsubopt: 0.686 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.583 RNAwolf: 0.511 Sensitivity Cylofold: 0.498 RNAwolf: 0.474 Positive Predictive Value Cylofold: 0.692 RNAwolf: 0.563 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.604 RNAwolf: 0.502 Sensitivity McQFold: 0.522 RNAwolf: 0.469 Positive Predictive Value McQFold: 0.707 RNAwolf: 0.546 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.523 RNAwolf: 0.370 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.344 Positive Predictive Value RNAalifold(seed): 0.800 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	38 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.574 RNAwolf: 0.512 Sensitivity Pknots: 0.516 RNAwolf: 0.479 Positive Predictive Value Pknots: 0.646 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	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: 7.8595327961e-05	4 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.471 RNAwolf: 0.416 Sensitivity RNASampler(seed): 0.341 RNAwolf: 0.403 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	8 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.489 RNAwolf: 0.364 Sensitivity RSpredict(20): 0.367 RNAwolf: 0.333 Positive Predictive Value RSpredict(20): 0.660 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.567 RNAwolf: 0.364 Sensitivity Mastr(20): 0.389 RNAwolf: 0.333 Positive Predictive Value Mastr(20): 0.833 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.537 RNAwolf: 0.512 Sensitivity Vsfold4: 0.458 RNAwolf: 0.479 Positive Predictive Value Vsfold4: 0.639 RNAwolf: 0.556 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.48494289621e-08	30 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.591 RNAwolf: 0.488 Sensitivity RNASLOpt: 0.498 RNAwolf: 0.457 Positive Predictive Value RNASLOpt: 0.709 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.540 RNAwolf: 0.364 Sensitivity Multilign(20): 0.456 RNAwolf: 0.333 Positive Predictive Value Multilign(20): 0.647 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.451 RNAwolf: 0.370 Sensitivity Murlet(seed): 0.268 RNAwolf: 0.344 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.571 RNAwolf: 0.517 Sensitivity MCFold: 0.599 RNAwolf: 0.490 Positive Predictive Value MCFold: 0.552 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.505 Vsfold5: 0.479 Sensitivity RNAwolf: 0.472 Vsfold5: 0.420 Positive Predictive Value RNAwolf: 0.550 Vsfold5: 0.557 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 1.5875416339e-07	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.530 RDfolder: 0.496 Sensitivity RNAwolf: 0.493 RDfolder: 0.388 Positive Predictive Value RNAwolf: 0.583 RDfolder: 0.647 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.33522642e-07	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.414 RSpredict(seed): 0.193 Sensitivity RNAwolf: 0.375 RSpredict(seed): 0.084 Positive Predictive Value RNAwolf: 0.467 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.414 PPfold(seed): 0.102 Sensitivity RNAwolf: 0.375 PPfold(seed): 0.020 Positive Predictive Value RNAwolf: 0.467 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.524 NanoFolder: 0.490 Sensitivity RNAwolf: 0.483 NanoFolder: 0.495 Positive Predictive Value RNAwolf: 0.578 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.24403703175e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.375 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.467 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-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	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.538 RNAwolf: 0.466 Sensitivity Multilign(seed): 0.420 RNAwolf: 0.413 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAwolf: 0.339 Sensitivity PETfold_pre2.0(seed): 0.551 RNAwolf: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAwolf: 0.384 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): 0.594 RNAwolf: 0.364 Sensitivity TurboFold(20): 0.470 RNAwolf: 0.333 Positive Predictive Value TurboFold(20): 0.756 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAwolf: 0.220 Sensitivity PETfold_pre2.0(20): 0.497 RNAwolf: 0.204 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAwolf: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAwolf: 0.344 Sensitivity TurboFold(seed): 0.422 RNAwolf: 0.316 Positive Predictive Value TurboFold(seed): 0.642 RNAwolf: 0.384 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): 0.665 RNAwolf: 0.364 Sensitivity PPfold(20): 0.519 RNAwolf: 0.333 Positive Predictive Value PPfold(20): 0.859 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.344 Carnac(seed): 0.123 Sensitivity RNAwolf: 0.316 Carnac(seed): 0.015 Positive Predictive Value RNAwolf: 0.384 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Murlet(seed)	26 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.671 Murlet(seed): 0.539 Sensitivity MXScarna(seed): 0.561 Murlet(seed): 0.337 Positive Predictive Value MXScarna(seed): 0.808 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.675 Murlet(seed): 0.540 Sensitivity CentroidFold: 0.578 Murlet(seed): 0.338 Positive Predictive Value CentroidFold: 0.794 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 Murlet(seed): 0.490 Sensitivity CentroidAlifold(20): 0.470 Murlet(seed): 0.269 Positive Predictive Value CentroidAlifold(20): 0.904 Murlet(seed): 0.899 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	17 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.595 Murlet(seed): 0.491 Sensitivity RNAalifold(20): 0.436 Murlet(seed): 0.269 Positive Predictive Value RNAalifold(20): 0.817 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	17 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.609 Murlet(seed): 0.491 Sensitivity RNASampler(20): 0.452 Murlet(seed): 0.269 Positive Predictive Value RNASampler(20): 0.825 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	26 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.682 Murlet(seed): 0.539 Sensitivity Sfold: 0.581 Murlet(seed): 0.337 Positive Predictive Value Sfold: 0.805 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.625 Murlet(seed): 0.491 Sensitivity MXScarna(20): 0.506 Murlet(seed): 0.269 Positive Predictive Value MXScarna(20): 0.775 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	26 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.654 Murlet(seed): 0.539 Sensitivity Contrafold: 0.582 Murlet(seed): 0.337 Positive Predictive Value Contrafold: 0.740 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	19 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.648 Murlet(seed): 0.542 Sensitivity Fold: 0.588 Murlet(seed): 0.339 Positive Predictive Value Fold: 0.719 Murlet(seed): 0.871 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.84041289224e-08	26 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.677 Murlet(seed): 0.539 Sensitivity HotKnots: 0.608 Murlet(seed): 0.337 Positive Predictive Value HotKnots: 0.759 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.573 Murlet(seed): 0.465 Sensitivity CentroidHomfold‑LAST: 0.450 Murlet(seed): 0.279 Positive Predictive Value CentroidHomfold‑LAST: 0.736 Murlet(seed): 0.780 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.505 Murlet(seed): 0.451 Sensitivity IPknot: 0.402 Murlet(seed): 0.268 Positive Predictive Value IPknot: 0.641 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	24 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.630 Murlet(seed): 0.538 Sensitivity MaxExpect: 0.561 Murlet(seed): 0.339 Positive Predictive Value MaxExpect: 0.713 Murlet(seed): 0.862 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.663 Murlet(seed): 0.539 Sensitivity UNAFold: 0.586 Murlet(seed): 0.337 Positive Predictive Value UNAFold: 0.754 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.488 Murlet(seed): 0.425 Sensitivity ContextFold: 0.376 Murlet(seed): 0.248 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	26 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.692 Murlet(seed): 0.539 Sensitivity RNAshapes: 0.614 Murlet(seed): 0.337 Positive Predictive Value RNAshapes: 0.783 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.678 Murlet(seed): 0.539 Sensitivity RNAfold: 0.604 Murlet(seed): 0.337 Positive Predictive Value RNAfold: 0.765 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.679 Murlet(seed): 0.539 Sensitivity PknotsRG: 0.609 Murlet(seed): 0.337 Positive Predictive Value PknotsRG: 0.762 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08	25 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 Murlet(seed): 0.540 Sensitivity CentroidAlifold(seed): 0.549 Murlet(seed): 0.338 Positive Predictive Value CentroidAlifold(seed): 0.883 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.557 Murlet(seed): 0.499 Sensitivity ProbKnot: 0.513 Murlet(seed): 0.292 Positive Predictive Value ProbKnot: 0.611 Murlet(seed): 0.857 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.80908287419e-08	17 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.550 Murlet(seed): 0.491 Sensitivity Murlet(20): 0.384 Murlet(seed): 0.269 Positive Predictive Value Murlet(20): 0.794 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	17 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.534 Murlet(seed): 0.491 Sensitivity Carnac(20): 0.302 Murlet(seed): 0.269 Positive Predictive Value Carnac(20): 0.951 Murlet(seed): 0.901 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.91441904741e-08	20 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.690 Murlet(seed): 0.553 Sensitivity Afold: 0.630 Murlet(seed): 0.367 Positive Predictive Value Afold: 0.760 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.624 Murlet(seed): 0.539 Sensitivity RNAsubopt: 0.562 Murlet(seed): 0.337 Positive Predictive Value RNAsubopt: 0.698 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	13 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.602 Murlet(seed): 0.502 Sensitivity Cylofold: 0.522 Murlet(seed): 0.300 Positive Predictive Value Cylofold: 0.701 Murlet(seed): 0.849 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	26 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.647 Murlet(seed): 0.539 Sensitivity McQFold: 0.570 Murlet(seed): 0.337 Positive Predictive Value McQFold: 0.740 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	26 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Murlet(seed): 0.539 Sensitivity RNAalifold(seed): 0.460 Murlet(seed): 0.337 Positive Predictive Value RNAalifold(seed): 0.905 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.628 Murlet(seed): 0.539 Sensitivity Pknots: 0.581 Murlet(seed): 0.337 Positive Predictive Value Pknots: 0.685 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-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: 2.66715895098e-08	17 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Murlet(seed): 0.564 Sensitivity RNASampler(seed): 0.535 Murlet(seed): 0.385 Positive Predictive Value RNASampler(seed): 0.851 Murlet(seed): 0.832 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	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	17 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.491 RSpredict(20): 0.468 Sensitivity Murlet(seed): 0.269 RSpredict(20): 0.347 Positive Predictive Value Murlet(seed): 0.901 RSpredict(20): 0.638 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.44854136456e-07	17 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.491 Mastr(20): 0.460 Sensitivity Murlet(seed): 0.269 Mastr(20): 0.272 Positive Predictive Value Murlet(seed): 0.901 Mastr(20): 0.784 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	26 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.539 Murlet(seed): 0.539 Sensitivity Vsfold4: 0.460 Murlet(seed): 0.337 Positive Predictive Value Vsfold4: 0.639 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.554240997957	5 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.425 RNASLOpt: 0.390 Sensitivity Murlet(seed): 0.248 RNASLOpt: 0.323 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.505 Multilign(20): 0.468 Sensitivity Murlet(seed): 0.279 Multilign(20): 0.378 Positive Predictive Value Murlet(seed): 0.921 Multilign(20): 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.451 RNAwolf: 0.370 Sensitivity Murlet(seed): 0.268 RNAwolf: 0.344 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		= Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.540 MCFold: 0.538 Sensitivity Murlet(seed): 0.341 MCFold: 0.554 Positive Predictive Value Murlet(seed): 0.862 MCFold: 0.529 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.523470400498	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.539 Vsfold5: 0.520 Sensitivity Murlet(seed): 0.337 Vsfold5: 0.455 Positive Predictive Value Murlet(seed): 0.868 Vsfold5: 0.602 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.36978958876e-05	= RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.593 Murlet(seed): 0.589 Sensitivity RDfolder: 0.483 Murlet(seed): 0.410 Positive Predictive Value RDfolder: 0.737 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.711548191155	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 RSpredict(seed): 0.459 Sensitivity Murlet(seed): 0.337 RSpredict(seed): 0.282 Positive Predictive Value Murlet(seed): 0.868 RSpredict(seed): 0.754 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.451 PPfold(seed): 0.133 Sensitivity Murlet(seed): 0.268 PPfold(seed): 0.033 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.403 NanoFolder: 0.280 Sensitivity Murlet(seed): 0.237 NanoFolder: 0.298 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 Mastr(seed): 0.365 Sensitivity Murlet(seed): 0.337 Mastr(seed): 0.149 Positive Predictive Value Murlet(seed): 0.868 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-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	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Murlet(seed): 0.447 Sensitivity Multilign(seed): 0.475 Murlet(seed): 0.285 Positive Predictive Value Multilign(seed): 0.750 Murlet(seed): 0.714 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 Murlet(seed): 0.425 Sensitivity PETfold_pre2.0(seed): 0.459 Murlet(seed): 0.248 Positive Predictive Value PETfold_pre2.0(seed): 0.726 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.590 Murlet(seed): 0.527 Sensitivity TurboFold(20): 0.469 Murlet(seed): 0.306 Positive Predictive Value TurboFold(20): 0.748 Murlet(seed): 0.914 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.539 PETfold_pre2.0(20): 0.527 Sensitivity Murlet(seed): 0.292 PETfold_pre2.0(20): 0.407 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Murlet(seed): 0.465 Sensitivity TurboFold(seed): 0.428 Murlet(seed): 0.279 Positive Predictive Value TurboFold(seed): 0.632 Murlet(seed): 0.780 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.605 Murlet(seed): 0.527 Sensitivity PPfold(20): 0.455 Murlet(seed): 0.306 Positive Predictive Value PPfold(20): 0.812 Murlet(seed): 0.914 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 Carnac(seed): 0.287 Sensitivity Murlet(seed): 0.337 Carnac(seed): 0.083 Positive Predictive Value Murlet(seed): 0.868 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08
MCFold	38 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.692 MCFold: 0.502 Sensitivity MXScarna(seed): 0.585 MCFold: 0.526 Positive Predictive Value MXScarna(seed): 0.824 MCFold: 0.487 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	96 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.703 MCFold: 0.566 Sensitivity CentroidFold: 0.615 MCFold: 0.588 Positive Predictive Value CentroidFold: 0.809 MCFold: 0.553 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.690 MCFold: 0.414 Sensitivity CentroidAlifold(20): 0.539 MCFold: 0.438 Positive Predictive Value CentroidAlifold(20): 0.888 MCFold: 0.399 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.652 MCFold: 0.421 Sensitivity RNAalifold(20): 0.513 MCFold: 0.445 Positive Predictive Value RNAalifold(20): 0.833 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	24 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.667 MCFold: 0.421 Sensitivity RNASampler(20): 0.522 MCFold: 0.445 Positive Predictive Value RNASampler(20): 0.857 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	109 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.706 MCFold: 0.577 Sensitivity Sfold: 0.617 MCFold: 0.597 Positive Predictive Value Sfold: 0.813 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.651 MCFold: 0.421 Sensitivity MXScarna(20): 0.546 MCFold: 0.445 Positive Predictive Value MXScarna(20): 0.779 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	109 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.689 MCFold: 0.577 Sensitivity Contrafold: 0.618 MCFold: 0.597 Positive Predictive Value Contrafold: 0.773 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.715 MCFold: 0.607 Sensitivity Fold: 0.651 MCFold: 0.627 Positive Predictive Value Fold: 0.791 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.698 MCFold: 0.577 Sensitivity HotKnots: 0.633 MCFold: 0.597 Positive Predictive Value HotKnots: 0.776 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 MCFold: 0.567 Sensitivity CentroidHomfold‑LAST: 0.530 MCFold: 0.593 Positive Predictive Value CentroidHomfold‑LAST: 0.863 MCFold: 0.552 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.688 MCFold: 0.571 Sensitivity IPknot: 0.589 MCFold: 0.599 Positive Predictive Value IPknot: 0.808 MCFold: 0.552 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.676 MCFold: 0.557 Sensitivity MaxExpect: 0.608 MCFold: 0.580 Positive Predictive Value MaxExpect: 0.758 MCFold: 0.543 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.700 MCFold: 0.577 Sensitivity UNAFold: 0.628 MCFold: 0.597 Positive Predictive Value UNAFold: 0.787 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.719 MCFold: 0.596 Sensitivity ContextFold: 0.613 MCFold: 0.626 Positive Predictive Value ContextFold: 0.848 MCFold: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	109 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.692 MCFold: 0.577 Sensitivity RNAshapes: 0.619 MCFold: 0.597 Positive Predictive Value RNAshapes: 0.780 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.691 MCFold: 0.577 Sensitivity RNAfold: 0.623 MCFold: 0.597 Positive Predictive Value RNAfold: 0.772 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.685 MCFold: 0.577 Sensitivity PknotsRG: 0.620 MCFold: 0.597 Positive Predictive Value PknotsRG: 0.763 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 MCFold: 0.498 Sensitivity CentroidAlifold(seed): 0.433 MCFold: 0.522 Positive Predictive Value CentroidAlifold(seed): 0.893 MCFold: 0.483 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.682 MCFold: 0.589 Sensitivity ProbKnot: 0.632 MCFold: 0.610 Positive Predictive Value ProbKnot: 0.741 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.602 MCFold: 0.421 Sensitivity Murlet(20): 0.454 MCFold: 0.445 Positive Predictive Value Murlet(20): 0.804 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.94031556815e-08	24 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.615 MCFold: 0.421 Sensitivity Carnac(20): 0.413 MCFold: 0.445 Positive Predictive Value Carnac(20): 0.921 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	86 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.688 MCFold: 0.617 Sensitivity Afold: 0.631 MCFold: 0.636 Positive Predictive Value Afold: 0.757 MCFold: 0.606 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.671 MCFold: 0.577 Sensitivity RNAsubopt: 0.605 MCFold: 0.597 Positive Predictive Value RNAsubopt: 0.750 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.656 MCFold: 0.579 Sensitivity Cylofold: 0.568 MCFold: 0.599 Positive Predictive Value Cylofold: 0.764 MCFold: 0.567 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.661 MCFold: 0.575 Sensitivity McQFold: 0.573 MCFold: 0.595 Positive Predictive Value McQFold: 0.769 MCFold: 0.563 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.629 MCFold: 0.547 Sensitivity RNAalifold(seed): 0.443 MCFold: 0.562 Positive Predictive Value RNAalifold(seed): 0.898 MCFold: 0.538 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	109 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.647 MCFold: 0.577 Sensitivity Pknots: 0.591 MCFold: 0.597 Positive Predictive Value Pknots: 0.716 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-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	17 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.673 MCFold: 0.595 Sensitivity RNASampler(seed): 0.535 MCFold: 0.619 Positive Predictive Value RNASampler(seed): 0.851 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.26346675981e-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: 3.56938820447e-08	24 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.580 MCFold: 0.421 Sensitivity RSpredict(20): 0.468 MCFold: 0.445 Positive Predictive Value RSpredict(20): 0.724 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	24 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.591 MCFold: 0.421 Sensitivity Mastr(20): 0.417 MCFold: 0.445 Positive Predictive Value Mastr(20): 0.844 MCFold: 0.406 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	109 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.593 MCFold: 0.577 Sensitivity Vsfold4: 0.507 MCFold: 0.597 Positive Predictive Value Vsfold4: 0.701 MCFold: 0.566 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.621 MCFold: 0.596 Sensitivity RNASLOpt: 0.535 MCFold: 0.626 Positive Predictive Value RNASLOpt: 0.727 MCFold: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	9 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.526 MCFold: 0.461 Sensitivity Multilign(20): 0.434 MCFold: 0.472 Positive Predictive Value Multilign(20): 0.643 MCFold: 0.458 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	36 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.571 RNAwolf: 0.517 Sensitivity MCFold: 0.599 RNAwolf: 0.490 Positive Predictive Value MCFold: 0.552 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.540 MCFold: 0.538 Sensitivity Murlet(seed): 0.341 MCFold: 0.554 Positive Predictive Value Murlet(seed): 0.862 MCFold: 0.529 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.523470400498		= MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.576 Vsfold5: 0.573 Sensitivity MCFold: 0.596 Vsfold5: 0.500 Positive Predictive Value MCFold: 0.564 Vsfold5: 0.665 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 0.00158471883626	- RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.615 MCFold: 0.604 Sensitivity RDfolder: 0.511 MCFold: 0.622 Positive Predictive Value RDfolder: 0.750 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 1.83595875043e-07	+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.502 RSpredict(seed): 0.358 Sensitivity MCFold: 0.526 RSpredict(seed): 0.195 Positive Predictive Value MCFold: 0.487 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.454 PPfold(seed): 0.115 Sensitivity MCFold: 0.471 PPfold(seed): 0.025 Positive Predictive Value MCFold: 0.446 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.636 NanoFolder: 0.522 Sensitivity MCFold: 0.654 NanoFolder: 0.538 Positive Predictive Value MCFold: 0.624 NanoFolder: 0.515 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.502 Mastr(seed): 0.304 Sensitivity MCFold: 0.526 Mastr(seed): 0.104 Positive Predictive Value MCFold: 0.487 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 38 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	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.588 MCFold: 0.558 Sensitivity Multilign(seed): 0.483 MCFold: 0.552 Positive Predictive Value Multilign(seed): 0.727 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.663 MCFold: 0.441 Sensitivity PETfold_pre2.0(seed): 0.549 MCFold: 0.469 Positive Predictive Value PETfold_pre2.0(seed): 0.807 MCFold: 0.423 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.630 MCFold: 0.498 Sensitivity TurboFold(20): 0.516 MCFold: 0.512 Positive Predictive Value TurboFold(20): 0.776 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.586 MCFold: 0.444 Sensitivity PETfold_pre2.0(20): 0.464 MCFold: 0.472 Positive Predictive Value PETfold_pre2.0(20): 0.744 MCFold: 0.424 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.550 MCFold: 0.497 Sensitivity TurboFold(seed): 0.465 MCFold: 0.510 Positive Predictive Value TurboFold(seed): 0.659 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.650 MCFold: 0.498 Sensitivity PPfold(20): 0.500 MCFold: 0.512 Positive Predictive Value PPfold(20): 0.849 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.534 Carnac(seed): 0.273 Sensitivity MCFold: 0.554 Carnac(seed): 0.075 Positive Predictive Value MCFold: 0.521 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08
Vsfold5	44 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.673 Vsfold5: 0.491 Sensitivity MXScarna(seed): 0.562 Vsfold5: 0.426 Positive Predictive Value MXScarna(seed): 0.809 Vsfold5: 0.570 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	103 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.675 Vsfold5: 0.526 Sensitivity CentroidFold: 0.590 Vsfold5: 0.457 Positive Predictive Value CentroidFold: 0.777 Vsfold5: 0.611 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Vsfold5: 0.418 Sensitivity CentroidAlifold(20): 0.520 Vsfold5: 0.358 Positive Predictive Value CentroidAlifold(20): 0.892 Vsfold5: 0.493 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.644 Vsfold5: 0.406 Sensitivity RNAalifold(20): 0.491 Vsfold5: 0.347 Positive Predictive Value RNAalifold(20): 0.849 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.634 Vsfold5: 0.406 Sensitivity RNASampler(20): 0.477 Vsfold5: 0.347 Positive Predictive Value RNASampler(20): 0.844 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	117 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.668 Vsfold5: 0.528 Sensitivity Sfold: 0.580 Vsfold5: 0.458 Positive Predictive Value Sfold: 0.774 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.628 Vsfold5: 0.406 Sensitivity MXScarna(20): 0.523 Vsfold5: 0.347 Positive Predictive Value MXScarna(20): 0.757 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	117 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.659 Vsfold5: 0.528 Sensitivity Contrafold: 0.591 Vsfold5: 0.458 Positive Predictive Value Contrafold: 0.739 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.678 Vsfold5: 0.538 Sensitivity Fold: 0.616 Vsfold5: 0.470 Positive Predictive Value Fold: 0.750 Vsfold5: 0.621 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.662 Vsfold5: 0.528 Sensitivity HotKnots: 0.599 Vsfold5: 0.458 Positive Predictive Value HotKnots: 0.736 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.665 Vsfold5: 0.487 Sensitivity CentroidHomfold‑LAST: 0.511 Vsfold5: 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.872 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.672 Vsfold5: 0.479 Sensitivity IPknot: 0.570 Vsfold5: 0.420 Positive Predictive Value IPknot: 0.799 Vsfold5: 0.557 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.652 Vsfold5: 0.519 Sensitivity MaxExpect: 0.586 Vsfold5: 0.451 Positive Predictive Value MaxExpect: 0.730 Vsfold5: 0.604 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.663 Vsfold5: 0.528 Sensitivity UNAFold: 0.594 Vsfold5: 0.458 Positive Predictive Value UNAFold: 0.746 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.704 Vsfold5: 0.468 Sensitivity ContextFold: 0.592 Vsfold5: 0.408 Positive Predictive Value ContextFold: 0.842 Vsfold5: 0.545 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	117 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.649 Vsfold5: 0.528 Sensitivity RNAshapes: 0.580 Vsfold5: 0.458 Positive Predictive Value RNAshapes: 0.732 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.650 Vsfold5: 0.528 Sensitivity RNAfold: 0.586 Vsfold5: 0.458 Positive Predictive Value RNAfold: 0.726 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.645 Vsfold5: 0.528 Sensitivity PknotsRG: 0.584 Vsfold5: 0.458 Positive Predictive Value PknotsRG: 0.718 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Vsfold5: 0.487 Sensitivity CentroidAlifold(seed): 0.419 Vsfold5: 0.423 Positive Predictive Value CentroidAlifold(seed): 0.878 Vsfold5: 0.566 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.645 Vsfold5: 0.516 Sensitivity ProbKnot: 0.596 Vsfold5: 0.451 Positive Predictive Value ProbKnot: 0.701 Vsfold5: 0.596 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.582 Vsfold5: 0.406 Sensitivity Murlet(20): 0.423 Vsfold5: 0.347 Positive Predictive Value Murlet(20): 0.804 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.582 Vsfold5: 0.406 Sensitivity Carnac(20): 0.371 Vsfold5: 0.347 Positive Predictive Value Carnac(20): 0.915 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	91 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.646 Vsfold5: 0.543 Sensitivity Afold: 0.594 Vsfold5: 0.473 Positive Predictive Value Afold: 0.708 Vsfold5: 0.629 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.634 Vsfold5: 0.528 Sensitivity RNAsubopt: 0.573 Vsfold5: 0.458 Positive Predictive Value RNAsubopt: 0.707 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.648 Vsfold5: 0.546 Sensitivity Cylofold: 0.559 Vsfold5: 0.475 Positive Predictive Value Cylofold: 0.758 Vsfold5: 0.637 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.618 Vsfold5: 0.526 Sensitivity McQFold: 0.539 Vsfold5: 0.456 Positive Predictive Value McQFold: 0.714 Vsfold5: 0.613 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.593 Vsfold5: 0.481 Sensitivity RNAalifold(seed): 0.397 Vsfold5: 0.421 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold5: 0.555 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	115 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.633 Vsfold5: 0.547 Sensitivity Pknots: 0.574 Vsfold5: 0.475 Positive Predictive Value Pknots: 0.705 Vsfold5: 0.639 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-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	17 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.673 Vsfold5: 0.621 Sensitivity RNASampler(seed): 0.535 Vsfold5: 0.559 Positive Predictive Value RNASampler(seed): 0.851 Vsfold5: 0.695 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-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	27 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.547 Vsfold5: 0.423 Sensitivity RSpredict(20): 0.428 Vsfold5: 0.363 Positive Predictive Value RSpredict(20): 0.702 Vsfold5: 0.499 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.525 Vsfold5: 0.406 Sensitivity Mastr(20): 0.346 Vsfold5: 0.347 Positive Predictive Value Mastr(20): 0.800 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	117 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.561 Vsfold5: 0.528 Sensitivity Vsfold4: 0.480 Vsfold5: 0.458 Positive Predictive Value Vsfold4: 0.662 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.586 Vsfold5: 0.468 Sensitivity RNASLOpt: 0.492 Vsfold5: 0.408 Positive Predictive Value RNASLOpt: 0.704 Vsfold5: 0.545 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	10 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.521 Vsfold5: 0.402 Sensitivity Multilign(20): 0.428 Vsfold5: 0.349 Positive Predictive Value Multilign(20): 0.643 Vsfold5: 0.472 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	37 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.505 Vsfold5: 0.479 Sensitivity RNAwolf: 0.472 Vsfold5: 0.420 Positive Predictive Value RNAwolf: 0.550 Vsfold5: 0.557 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 1.5875416339e-07	26 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.539 Vsfold5: 0.520 Sensitivity Murlet(seed): 0.337 Vsfold5: 0.455 Positive Predictive Value Murlet(seed): 0.868 Vsfold5: 0.602 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.36978958876e-05	108 MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.576 Vsfold5: 0.573 Sensitivity MCFold: 0.596 Vsfold5: 0.500 Positive Predictive Value MCFold: 0.564 Vsfold5: 0.665 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 0.00158471883626		+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.631 RDfolder: 0.596 Sensitivity Vsfold5: 0.549 RDfolder: 0.495 Positive Predictive Value Vsfold5: 0.734 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.491 RSpredict(seed): 0.314 Sensitivity Vsfold5: 0.426 RSpredict(seed): 0.161 Positive Predictive Value Vsfold5: 0.570 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.404 PPfold(seed): 0.102 Sensitivity Vsfold5: 0.345 PPfold(seed): 0.020 Positive Predictive Value Vsfold5: 0.482 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.47941000302e-08	- NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.478 Vsfold5: 0.462 Sensitivity NanoFolder: 0.484 Vsfold5: 0.403 Positive Predictive Value NanoFolder: 0.482 Vsfold5: 0.539 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.98533417679e-07	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.477 Mastr(seed): 0.258 Sensitivity Vsfold5: 0.413 Mastr(seed): 0.075 Positive Predictive Value Vsfold5: 0.555 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 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	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.593 Vsfold5: 0.380 Sensitivity Multilign(seed): 0.475 Vsfold5: 0.316 Positive Predictive Value Multilign(seed): 0.750 Vsfold5: 0.472 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold5: 0.372 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold5: 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold5: 0.443 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.620 Vsfold5: 0.461 Sensitivity TurboFold(20): 0.500 Vsfold5: 0.400 Positive Predictive Value TurboFold(20): 0.775 Vsfold5: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold5: 0.384 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold5: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold5: 0.448 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.550 Vsfold5: 0.409 Sensitivity TurboFold(seed): 0.456 Vsfold5: 0.353 Positive Predictive Value TurboFold(seed): 0.672 Vsfold5: 0.483 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): 0.663 Vsfold5: 0.461 Sensitivity PPfold(20): 0.514 Vsfold5: 0.400 Positive Predictive Value PPfold(20): 0.861 Vsfold5: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.503 Carnac(seed): 0.260 Sensitivity Vsfold5: 0.437 Carnac(seed): 0.068 Positive Predictive Value Vsfold5: 0.585 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	31 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.714 RDfolder: 0.556 Sensitivity MXScarna(seed): 0.598 RDfolder: 0.462 Positive Predictive Value MXScarna(seed): 0.858 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	79 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.733 RDfolder: 0.581 Sensitivity CentroidFold: 0.638 RDfolder: 0.483 Positive Predictive Value CentroidFold: 0.850 RDfolder: 0.708 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.742 RDfolder: 0.517 Sensitivity CentroidAlifold(20): 0.588 RDfolder: 0.419 Positive Predictive Value CentroidAlifold(20): 0.941 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	16 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.712 RDfolder: 0.529 Sensitivity RNAalifold(20): 0.555 RDfolder: 0.431 Positive Predictive Value RNAalifold(20): 0.918 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.00627773251e-08	16 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.744 RDfolder: 0.529 Sensitivity RNASampler(20): 0.587 RDfolder: 0.431 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	92 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.717 RDfolder: 0.596 Sensitivity Sfold: 0.624 RDfolder: 0.495 Positive Predictive Value Sfold: 0.833 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.695 RDfolder: 0.529 Sensitivity MXScarna(20): 0.564 RDfolder: 0.431 Positive Predictive Value MXScarna(20): 0.862 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.39551335374e-08	92 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.726 RDfolder: 0.596 Sensitivity Contrafold: 0.644 RDfolder: 0.495 Positive Predictive Value Contrafold: 0.825 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.731 RDfolder: 0.622 Sensitivity Fold: 0.663 RDfolder: 0.524 Positive Predictive Value Fold: 0.812 RDfolder: 0.746 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.723 RDfolder: 0.596 Sensitivity HotKnots: 0.650 RDfolder: 0.495 Positive Predictive Value HotKnots: 0.813 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.706 RDfolder: 0.538 Sensitivity CentroidHomfold‑LAST: 0.542 RDfolder: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.927 RDfolder: 0.693 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.659 RDfolder: 0.496 Sensitivity IPknot: 0.550 RDfolder: 0.388 Positive Predictive Value IPknot: 0.799 RDfolder: 0.647 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	73 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.703 RDfolder: 0.590 Sensitivity MaxExpect: 0.627 RDfolder: 0.490 Positive Predictive Value MaxExpect: 0.796 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.719 RDfolder: 0.596 Sensitivity UNAFold: 0.639 RDfolder: 0.495 Positive Predictive Value UNAFold: 0.817 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.669 RDfolder: 0.481 Sensitivity ContextFold: 0.561 RDfolder: 0.379 Positive Predictive Value ContextFold: 0.807 RDfolder: 0.623 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	92 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.698 RDfolder: 0.596 Sensitivity RNAshapes: 0.617 RDfolder: 0.495 Positive Predictive Value RNAshapes: 0.797 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.707 RDfolder: 0.596 Sensitivity RNAfold: 0.631 RDfolder: 0.495 Positive Predictive Value RNAfold: 0.799 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.704 RDfolder: 0.596 Sensitivity PknotsRG: 0.631 RDfolder: 0.495 Positive Predictive Value PknotsRG: 0.795 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.611 RDfolder: 0.550 Sensitivity CentroidAlifold(seed): 0.435 RDfolder: 0.456 Positive Predictive Value CentroidAlifold(seed): 0.866 RDfolder: 0.672 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.710 RDfolder: 0.609 Sensitivity ProbKnot: 0.657 RDfolder: 0.514 Positive Predictive Value ProbKnot: 0.776 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.651 RDfolder: 0.529 Sensitivity Murlet(20): 0.490 RDfolder: 0.431 Positive Predictive Value Murlet(20): 0.871 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	16 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.617 RDfolder: 0.529 Sensitivity Carnac(20): 0.422 RDfolder: 0.431 Positive Predictive Value Carnac(20): 0.908 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.39162260866e-08	71 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.712 RDfolder: 0.629 Sensitivity Afold: 0.648 RDfolder: 0.529 Positive Predictive Value Afold: 0.789 RDfolder: 0.758 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.691 RDfolder: 0.596 Sensitivity RNAsubopt: 0.614 RDfolder: 0.495 Positive Predictive Value RNAsubopt: 0.784 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.706 RDfolder: 0.588 Sensitivity Cylofold: 0.613 RDfolder: 0.494 Positive Predictive Value Cylofold: 0.821 RDfolder: 0.710 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.596 Sensitivity McQFold: 0.604 RDfolder: 0.495 Positive Predictive Value McQFold: 0.831 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.668 RDfolder: 0.603 Sensitivity RNAalifold(seed): 0.509 RDfolder: 0.493 Positive Predictive Value RNAalifold(seed): 0.884 RDfolder: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	92 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.596 Sensitivity Pknots: 0.628 RDfolder: 0.495 Positive Predictive Value Pknots: 0.781 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-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	14 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.753 RDfolder: 0.674 Sensitivity RNASampler(seed): 0.603 RDfolder: 0.552 Positive Predictive Value RNASampler(seed): 0.946 RDfolder: 0.831 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	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: 5.19332990918e-08	16 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.623 RDfolder: 0.529 Sensitivity RSpredict(20): 0.472 RDfolder: 0.431 Positive Predictive Value RSpredict(20): 0.829 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.08252958266e-08	16 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.655 RDfolder: 0.529 Sensitivity Mastr(20): 0.503 RDfolder: 0.431 Positive Predictive Value Mastr(20): 0.858 RDfolder: 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08	92 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.655 RDfolder: 0.596 Sensitivity Vsfold4: 0.559 RDfolder: 0.495 Positive Predictive Value Vsfold4: 0.777 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.571 RDfolder: 0.481 Sensitivity RNASLOpt: 0.462 RDfolder: 0.379 Positive Predictive Value RNASLOpt: 0.718 RDfolder: 0.623 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	7 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.626 RDfolder: 0.478 Sensitivity Multilign(20): 0.517 RDfolder: 0.360 Positive Predictive Value Multilign(20): 0.766 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.530 RDfolder: 0.496 Sensitivity RNAwolf: 0.493 RDfolder: 0.388 Positive Predictive Value RNAwolf: 0.583 RDfolder: 0.647 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.33522642e-07	20 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.593 Murlet(seed): 0.589 Sensitivity RDfolder: 0.483 Murlet(seed): 0.410 Positive Predictive Value RDfolder: 0.737 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.711548191155	89 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.615 MCFold: 0.604 Sensitivity RDfolder: 0.511 MCFold: 0.622 Positive Predictive Value RDfolder: 0.750 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 1.83595875043e-07	92 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.631 RDfolder: 0.596 Sensitivity Vsfold5: 0.549 RDfolder: 0.495 Positive Predictive Value Vsfold5: 0.734 RDfolder: 0.727 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.556 RSpredict(seed): 0.440 Sensitivity RDfolder: 0.462 RSpredict(seed): 0.265 Positive Predictive Value RDfolder: 0.678 RSpredict(seed): 0.742 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.342 PPfold(seed): 0.138 Sensitivity RDfolder: 0.253 PPfold(seed): 0.026 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.561 RDfolder: 0.477 Sensitivity NanoFolder: 0.542 RDfolder: 0.392 Positive Predictive Value NanoFolder: 0.593 RDfolder: 0.594 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.556 Mastr(seed): 0.357 Sensitivity RDfolder: 0.462 Mastr(seed): 0.143 Positive Predictive Value RDfolder: 0.678 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 31 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	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.593 RDfolder: 0.476 Sensitivity Multilign(seed): 0.475 RDfolder: 0.361 Positive Predictive Value Multilign(seed): 0.750 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.634 RDfolder: 0.281 Sensitivity PETfold_pre2.0(seed): 0.515 RDfolder: 0.215 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.679 RDfolder: 0.478 Sensitivity TurboFold(20): 0.537 RDfolder: 0.360 Positive Predictive Value TurboFold(20): 0.865 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 RDfolder: 0.387 Sensitivity PETfold_pre2.0(20): 0.513 RDfolder: 0.288 Positive Predictive Value PETfold_pre2.0(20): 0.872 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? 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	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.702 RDfolder: 0.478 Sensitivity PPfold(20): 0.542 RDfolder: 0.360 Positive Predictive Value PPfold(20): 0.917 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.593 Carnac(seed): 0.351 Sensitivity RDfolder: 0.483 Carnac(seed): 0.125 Positive Predictive Value RDfolder: 0.737 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08
RSpredict(seed)	44 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.673 RSpredict(seed): 0.314 Sensitivity MXScarna(seed): 0.562 RSpredict(seed): 0.161 Positive Predictive Value MXScarna(seed): 0.809 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.625 RSpredict(seed): 0.308 Sensitivity CentroidFold: 0.545 RSpredict(seed): 0.156 Positive Predictive Value CentroidFold: 0.719 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 RSpredict(seed): 0.237 Sensitivity CentroidAlifold(20): 0.520 RSpredict(seed): 0.103 Positive Predictive Value CentroidAlifold(20): 0.892 RSpredict(seed): 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(seed): 0.249 Sensitivity RNAalifold(20): 0.491 RSpredict(seed): 0.110 Positive Predictive Value RNAalifold(20): 0.843 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RSpredict(seed): 0.249 Sensitivity RNASampler(20): 0.489 RSpredict(seed): 0.110 Positive Predictive Value RNASampler(20): 0.843 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.608 RSpredict(seed): 0.314 Sensitivity Sfold: 0.525 RSpredict(seed): 0.161 Positive Predictive Value Sfold: 0.708 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.634 RSpredict(seed): 0.249 Sensitivity MXScarna(20): 0.530 RSpredict(seed): 0.110 Positive Predictive Value MXScarna(20): 0.761 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.599 RSpredict(seed): 0.314 Sensitivity Contrafold: 0.544 RSpredict(seed): 0.161 Positive Predictive Value Contrafold: 0.664 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.625 RSpredict(seed): 0.288 Sensitivity Fold: 0.569 RSpredict(seed): 0.145 Positive Predictive Value Fold: 0.690 RSpredict(seed): 0.578 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.601 RSpredict(seed): 0.314 Sensitivity HotKnots: 0.549 RSpredict(seed): 0.161 Positive Predictive Value HotKnots: 0.663 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 RSpredict(seed): 0.226 Sensitivity CentroidHomfold‑LAST: 0.501 RSpredict(seed): 0.106 Positive Predictive Value CentroidHomfold‑LAST: 0.808 RSpredict(seed): 0.494 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.43692248862e-08	11 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.590 RSpredict(seed): 0.193 Sensitivity IPknot: 0.471 RSpredict(seed): 0.084 Positive Predictive Value IPknot: 0.747 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.25253056981e-08	40 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.605 RSpredict(seed): 0.306 Sensitivity MaxExpect: 0.543 RSpredict(seed): 0.156 Positive Predictive Value MaxExpect: 0.677 RSpredict(seed): 0.607 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.599 RSpredict(seed): 0.314 Sensitivity UNAFold: 0.540 RSpredict(seed): 0.161 Positive Predictive Value UNAFold: 0.667 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.616 RSpredict(seed): 0.110 Sensitivity ContextFold: 0.476 RSpredict(seed): 0.047 Positive Predictive Value ContextFold: 0.801 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	44 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.597 RSpredict(seed): 0.314 Sensitivity RNAshapes: 0.537 RSpredict(seed): 0.161 Positive Predictive Value RNAshapes: 0.668 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.603 RSpredict(seed): 0.314 Sensitivity RNAfold: 0.548 RSpredict(seed): 0.161 Positive Predictive Value RNAfold: 0.667 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.602 RSpredict(seed): 0.314 Sensitivity PknotsRG: 0.549 RSpredict(seed): 0.161 Positive Predictive Value PknotsRG: 0.665 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 RSpredict(seed): 0.308 Sensitivity CentroidAlifold(seed): 0.419 RSpredict(seed): 0.156 Positive Predictive Value CentroidAlifold(seed): 0.878 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.570 RSpredict(seed): 0.228 Sensitivity ProbKnot: 0.529 RSpredict(seed): 0.106 Positive Predictive Value ProbKnot: 0.618 RSpredict(seed): 0.498 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.582 RSpredict(seed): 0.249 Sensitivity Murlet(20): 0.425 RSpredict(seed): 0.110 Positive Predictive Value Murlet(20): 0.800 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.586 RSpredict(seed): 0.249 Sensitivity Carnac(20): 0.377 RSpredict(seed): 0.110 Positive Predictive Value Carnac(20): 0.916 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.570 RSpredict(seed): 0.374 Sensitivity Afold: 0.534 RSpredict(seed): 0.208 Positive Predictive Value Afold: 0.613 RSpredict(seed): 0.677 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(seed): 0.314 Sensitivity RNAsubopt: 0.521 RSpredict(seed): 0.161 Positive Predictive Value RNAsubopt: 0.627 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.640 RSpredict(seed): 0.274 Sensitivity Cylofold: 0.553 RSpredict(seed): 0.137 Positive Predictive Value Cylofold: 0.747 RSpredict(seed): 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.565 RSpredict(seed): 0.314 Sensitivity McQFold: 0.500 RSpredict(seed): 0.161 Positive Predictive Value McQFold: 0.643 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 RSpredict(seed): 0.404 Sensitivity RNAalifold(seed): 0.397 RSpredict(seed): 0.232 Positive Predictive Value RNAalifold(seed): 0.887 RSpredict(seed): 0.708 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	42 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.615 RSpredict(seed): 0.334 Sensitivity Pknots: 0.562 RSpredict(seed): 0.176 Positive Predictive Value Pknots: 0.679 RSpredict(seed): 0.646 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-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: 5.23657817852e-08	17 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 RSpredict(seed): 0.555 Sensitivity RNASampler(seed): 0.535 RSpredict(seed): 0.390 Positive Predictive Value RNASampler(seed): 0.851 RSpredict(seed): 0.795 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-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	27 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.547 RSpredict(seed): 0.249 Sensitivity RSpredict(20): 0.428 RSpredict(seed): 0.110 Positive Predictive Value RSpredict(20): 0.702 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.527 RSpredict(seed): 0.249 Sensitivity Mastr(20): 0.348 RSpredict(seed): 0.110 Positive Predictive Value Mastr(20): 0.803 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.517 RSpredict(seed): 0.314 Sensitivity Vsfold4: 0.445 RSpredict(seed): 0.161 Positive Predictive Value Vsfold4: 0.605 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RSpredict(seed): 0.110 Sensitivity RNASLOpt: 0.374 RSpredict(seed): 0.047 Positive Predictive Value RNASLOpt: 0.609 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.521 RSpredict(seed): 0.304 Sensitivity Multilign(20): 0.428 RSpredict(seed): 0.142 Positive Predictive Value Multilign(20): 0.643 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	11 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.414 RSpredict(seed): 0.193 Sensitivity RNAwolf: 0.375 RSpredict(seed): 0.084 Positive Predictive Value RNAwolf: 0.467 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	26 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 RSpredict(seed): 0.459 Sensitivity Murlet(seed): 0.337 RSpredict(seed): 0.282 Positive Predictive Value Murlet(seed): 0.868 RSpredict(seed): 0.754 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.502 RSpredict(seed): 0.358 Sensitivity MCFold: 0.526 RSpredict(seed): 0.195 Positive Predictive Value MCFold: 0.487 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.491 RSpredict(seed): 0.314 Sensitivity Vsfold5: 0.426 RSpredict(seed): 0.161 Positive Predictive Value Vsfold5: 0.570 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.556 RSpredict(seed): 0.440 Sensitivity RDfolder: 0.462 RSpredict(seed): 0.265 Positive Predictive Value RDfolder: 0.678 RSpredict(seed): 0.742 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.193 PPfold(seed): 0.102 Sensitivity RSpredict(seed): 0.084 PPfold(seed): 0.020 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.95437096897e-08	? NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.346 RSpredict(seed): 0.090 Sensitivity NanoFolder: 0.353 RSpredict(seed): 0.038 Positive Predictive Value NanoFolder: 0.349 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.314 Mastr(seed): 0.263 Sensitivity RSpredict(seed): 0.161 Mastr(seed): 0.077 Positive Predictive Value RSpredict(seed): 0.620 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 44 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	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 RSpredict(seed): 0.364 Sensitivity Multilign(seed): 0.475 RSpredict(seed): 0.215 Positive Predictive Value Multilign(seed): 0.750 RSpredict(seed): 0.630 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RSpredict(seed): 0.110 Sensitivity PETfold_pre2.0(seed): 0.551 RSpredict(seed): 0.047 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.620 RSpredict(seed): 0.299 Sensitivity TurboFold(20): 0.500 RSpredict(seed): 0.138 Positive Predictive Value TurboFold(20): 0.775 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(seed): 0.184 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(seed): 0.072 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 RSpredict(seed): 0.278 Sensitivity TurboFold(seed): 0.456 RSpredict(seed): 0.141 Positive Predictive Value TurboFold(seed): 0.672 RSpredict(seed): 0.556 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(seed): 0.299 Sensitivity PPfold(20): 0.514 RSpredict(seed): 0.138 Positive Predictive Value PPfold(20): 0.861 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.404 Carnac(seed): 0.260 Sensitivity RSpredict(seed): 0.231 Carnac(seed): 0.068 Positive Predictive Value RSpredict(seed): 0.713 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08
PPfold(seed)	11 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.624 PPfold(seed): 0.102 Sensitivity MXScarna(seed): 0.493 PPfold(seed): 0.020 Positive Predictive Value MXScarna(seed): 0.796 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	11 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.578 PPfold(seed): 0.102 Sensitivity CentroidFold: 0.465 PPfold(seed): 0.020 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	8 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(seed): 0.026 Sensitivity CentroidAlifold(20): 0.515 PPfold(seed): 0.004 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 PPfold(seed): 0.026 Sensitivity RNAalifold(20): 0.481 PPfold(seed): 0.004 Positive Predictive Value RNAalifold(20): 0.823 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 PPfold(seed): 0.026 Sensitivity RNASampler(20): 0.478 PPfold(seed): 0.004 Positive Predictive Value RNASampler(20): 0.854 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.539 PPfold(seed): 0.102 Sensitivity Sfold: 0.426 PPfold(seed): 0.020 Positive Predictive Value Sfold: 0.691 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.45186852942e-09	8 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.586 PPfold(seed): 0.026 Sensitivity MXScarna(20): 0.474 PPfold(seed): 0.004 Positive Predictive Value MXScarna(20): 0.731 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.559 PPfold(seed): 0.102 Sensitivity Contrafold: 0.471 PPfold(seed): 0.020 Positive Predictive Value Contrafold: 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	11 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.516 PPfold(seed): 0.102 Sensitivity Fold: 0.443 PPfold(seed): 0.020 Positive Predictive Value Fold: 0.610 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	11 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.566 PPfold(seed): 0.102 Sensitivity HotKnots: 0.487 PPfold(seed): 0.020 Positive Predictive Value HotKnots: 0.664 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	11 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 PPfold(seed): 0.102 Sensitivity CentroidHomfold‑LAST: 0.479 PPfold(seed): 0.020 Positive Predictive Value CentroidHomfold‑LAST: 0.795 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.07842257011e-08	11 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.590 PPfold(seed): 0.102 Sensitivity IPknot: 0.471 PPfold(seed): 0.020 Positive Predictive Value IPknot: 0.747 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.09700314043e-09	11 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.513 PPfold(seed): 0.102 Sensitivity MaxExpect: 0.434 PPfold(seed): 0.020 Positive Predictive Value MaxExpect: 0.615 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	11 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.490 PPfold(seed): 0.102 Sensitivity UNAFold: 0.417 PPfold(seed): 0.020 Positive Predictive Value UNAFold: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	8 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.616 PPfold(seed): 0.121 Sensitivity ContextFold: 0.476 PPfold(seed): 0.028 Positive Predictive Value ContextFold: 0.801 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.537 PPfold(seed): 0.102 Sensitivity RNAshapes: 0.454 PPfold(seed): 0.020 Positive Predictive Value RNAshapes: 0.643 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	11 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.565 PPfold(seed): 0.102 Sensitivity RNAfold: 0.476 PPfold(seed): 0.020 Positive Predictive Value RNAfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.40919803867e-08	11 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.600 PPfold(seed): 0.102 Sensitivity PknotsRG: 0.513 PPfold(seed): 0.020 Positive Predictive Value PknotsRG: 0.709 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.69265863073e-08	11 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 PPfold(seed): 0.102 Sensitivity CentroidAlifold(seed): 0.347 PPfold(seed): 0.020 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.00627773251e-08	11 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.513 PPfold(seed): 0.102 Sensitivity ProbKnot: 0.457 PPfold(seed): 0.020 Positive Predictive Value ProbKnot: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.84361416392e-08	8 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.581 PPfold(seed): 0.026 Sensitivity Murlet(20): 0.433 PPfold(seed): 0.004 Positive Predictive Value Murlet(20): 0.785 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.560 PPfold(seed): 0.026 Sensitivity Carnac(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.489 PPfold(seed): 0.187 Sensitivity Afold: 0.443 PPfold(seed): 0.066 Positive Predictive Value Afold: 0.547 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.500 PPfold(seed): 0.102 Sensitivity RNAsubopt: 0.429 PPfold(seed): 0.020 Positive Predictive Value RNAsubopt: 0.591 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	9 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.630 PPfold(seed): 0.128 Sensitivity Cylofold: 0.519 PPfold(seed): 0.022 Positive Predictive Value Cylofold: 0.773 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.539 PPfold(seed): 0.102 Sensitivity McQFold: 0.462 PPfold(seed): 0.020 Positive Predictive Value McQFold: 0.637 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.35333035499e-09	7 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 PPfold(seed): 0.133 Sensitivity RNAalifold(seed): 0.344 PPfold(seed): 0.033 Positive Predictive Value RNAalifold(seed): 0.800 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.532 PPfold(seed): 0.102 Sensitivity Pknots: 0.462 PPfold(seed): 0.020 Positive Predictive Value Pknots: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.70361883708e-09	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	4 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 PPfold(seed): 0.169 Sensitivity RNASampler(seed): 0.341 PPfold(seed): 0.054 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	8 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 PPfold(seed): 0.026 Sensitivity RSpredict(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value RSpredict(20): 0.660 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.567 PPfold(seed): 0.026 Sensitivity Mastr(20): 0.389 PPfold(seed): 0.004 Positive Predictive Value Mastr(20): 0.833 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.454 PPfold(seed): 0.102 Sensitivity Vsfold4: 0.367 PPfold(seed): 0.020 Positive Predictive Value Vsfold4: 0.570 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	8 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 PPfold(seed): 0.121 Sensitivity RNASLOpt: 0.374 PPfold(seed): 0.028 Positive Predictive Value RNASLOpt: 0.609 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.540 PPfold(seed): 0.026 Sensitivity Multilign(20): 0.456 PPfold(seed): 0.004 Positive Predictive Value Multilign(20): 0.647 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.414 PPfold(seed): 0.102 Sensitivity RNAwolf: 0.375 PPfold(seed): 0.020 Positive Predictive Value RNAwolf: 0.467 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	7 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.451 PPfold(seed): 0.133 Sensitivity Murlet(seed): 0.268 PPfold(seed): 0.033 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.454 PPfold(seed): 0.115 Sensitivity MCFold: 0.471 PPfold(seed): 0.025 Positive Predictive Value MCFold: 0.446 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.404 PPfold(seed): 0.102 Sensitivity Vsfold5: 0.345 PPfold(seed): 0.020 Positive Predictive Value Vsfold5: 0.482 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.47941000302e-08	8 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.342 PPfold(seed): 0.138 Sensitivity RDfolder: 0.253 PPfold(seed): 0.026 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.193 PPfold(seed): 0.102 Sensitivity RSpredict(seed): 0.084 PPfold(seed): 0.020 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.95437096897e-08		? NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.346 PPfold(seed): 0.125 Sensitivity NanoFolder: 0.353 PPfold(seed): 0.030 Positive Predictive Value NanoFolder: 0.349 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.102 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.020 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-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	? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 PPfold(seed): 0.179 Sensitivity Multilign(seed): 0.420 PPfold(seed): 0.043 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PPfold(seed): 0.121 Sensitivity PETfold_pre2.0(seed): 0.551 PPfold(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 PPfold(seed): 0.026 Sensitivity TurboFold(20): 0.470 PPfold(seed): 0.004 Positive Predictive Value TurboFold(20): 0.756 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(seed): 0.034 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(seed): 0.006 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 PPfold(seed): 0.118 Sensitivity TurboFold(seed): 0.422 PPfold(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.642 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 PPfold(seed): 0.026 Sensitivity PPfold(20): 0.519 PPfold(seed): 0.004 Positive Predictive Value PPfold(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.123 PPfold(seed): 0.118 Sensitivity Carnac(seed): 0.015 PPfold(seed): 0.027 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
NanoFolder	7 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.594 NanoFolder: 0.346 Sensitivity MXScarna(seed): 0.468 NanoFolder: 0.353 Positive Predictive Value MXScarna(seed): 0.759 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.663 NanoFolder: 0.490 Sensitivity CentroidFold: 0.567 NanoFolder: 0.495 Positive Predictive Value CentroidFold: 0.782 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	4 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.646 NanoFolder: 0.316 Sensitivity CentroidAlifold(20): 0.473 NanoFolder: 0.324 Positive Predictive Value CentroidAlifold(20): 0.886 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.565 NanoFolder: 0.316 Sensitivity RNAalifold(20): 0.432 NanoFolder: 0.324 Positive Predictive Value RNAalifold(20): 0.744 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.567 NanoFolder: 0.316 Sensitivity RNASampler(20): 0.426 NanoFolder: 0.324 Positive Predictive Value RNASampler(20): 0.759 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.614 NanoFolder: 0.490 Sensitivity Sfold: 0.520 NanoFolder: 0.495 Positive Predictive Value Sfold: 0.733 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	4 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.524 NanoFolder: 0.316 Sensitivity MXScarna(20): 0.439 NanoFolder: 0.324 Positive Predictive Value MXScarna(20): 0.631 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.656 NanoFolder: 0.490 Sensitivity Contrafold: 0.574 NanoFolder: 0.495 Positive Predictive Value Contrafold: 0.756 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	17 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.629 NanoFolder: 0.490 Sensitivity Fold: 0.559 NanoFolder: 0.495 Positive Predictive Value Fold: 0.714 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	17 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.630 NanoFolder: 0.490 Sensitivity HotKnots: 0.567 NanoFolder: 0.495 Positive Predictive Value HotKnots: 0.708 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	16 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.613 NanoFolder: 0.473 Sensitivity CentroidHomfold‑LAST: 0.482 NanoFolder: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.787 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.95070920198e-08	17 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.678 NanoFolder: 0.490 Sensitivity IPknot: 0.576 NanoFolder: 0.495 Positive Predictive Value IPknot: 0.804 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	17 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.601 NanoFolder: 0.490 Sensitivity MaxExpect: 0.530 NanoFolder: 0.495 Positive Predictive Value MaxExpect: 0.689 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	17 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.576 NanoFolder: 0.490 Sensitivity UNAFold: 0.515 NanoFolder: 0.495 Positive Predictive Value UNAFold: 0.653 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.706 NanoFolder: 0.490 Sensitivity ContextFold: 0.584 NanoFolder: 0.495 Positive Predictive Value ContextFold: 0.859 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	17 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.616 NanoFolder: 0.490 Sensitivity RNAshapes: 0.547 NanoFolder: 0.495 Positive Predictive Value RNAshapes: 0.700 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	17 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.639 NanoFolder: 0.490 Sensitivity RNAfold: 0.567 NanoFolder: 0.495 Positive Predictive Value RNAfold: 0.728 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.642 NanoFolder: 0.490 Sensitivity PknotsRG: 0.574 NanoFolder: 0.495 Positive Predictive Value PknotsRG: 0.724 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.32883086441e-08	7 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.533 NanoFolder: 0.346 Sensitivity CentroidAlifold(seed): 0.289 NanoFolder: 0.353 Positive Predictive Value CentroidAlifold(seed): 0.986 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.606 NanoFolder: 0.490 Sensitivity ProbKnot: 0.552 NanoFolder: 0.495 Positive Predictive Value ProbKnot: 0.673 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.48104284388e-08	4 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.503 NanoFolder: 0.316 Sensitivity Murlet(20): 0.372 NanoFolder: 0.324 Positive Predictive Value Murlet(20): 0.688 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.506 NanoFolder: 0.316 Sensitivity Carnac(20): 0.318 NanoFolder: 0.324 Positive Predictive Value Carnac(20): 0.810 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	12 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.683 NanoFolder: 0.548 Sensitivity Afold: 0.643 NanoFolder: 0.576 Positive Predictive Value Afold: 0.731 NanoFolder: 0.529 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.22210847902e-08	17 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.575 NanoFolder: 0.490 Sensitivity RNAsubopt: 0.517 NanoFolder: 0.495 Positive Predictive Value RNAsubopt: 0.646 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	14 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.620 NanoFolder: 0.546 Sensitivity Cylofold: 0.526 NanoFolder: 0.539 Positive Predictive Value Cylofold: 0.740 NanoFolder: 0.565 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	16 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.567 NanoFolder: 0.473 Sensitivity McQFold: 0.500 NanoFolder: 0.479 Positive Predictive Value McQFold: 0.650 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.34821445183e-08	4 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.459 NanoFolder: 0.280 Sensitivity RNAalifold(seed): 0.289 NanoFolder: 0.298 Positive Predictive Value RNAalifold(seed): 0.733 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.515 NanoFolder: 0.490 Sensitivity Pknots: 0.463 NanoFolder: 0.495 Positive Predictive Value Pknots: 0.582 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.65348477097e-08	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	2 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.198 NanoFolder: 0.171 Sensitivity RNASampler(seed): 0.151 NanoFolder: 0.208 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 2 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: 1.70887622364e-08	4 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.337 NanoFolder: 0.316 Sensitivity RSpredict(20): 0.243 NanoFolder: 0.324 Positive Predictive Value RSpredict(20): 0.474 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.499 NanoFolder: 0.316 Sensitivity Mastr(20): 0.324 NanoFolder: 0.324 Positive Predictive Value Mastr(20): 0.774 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.528 NanoFolder: 0.490 Sensitivity Vsfold4: 0.451 NanoFolder: 0.495 Positive Predictive Value Vsfold4: 0.627 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.30295446166e-08	17 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.591 NanoFolder: 0.490 Sensitivity RNASLOpt: 0.500 NanoFolder: 0.495 Positive Predictive Value RNASLOpt: 0.705 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	4 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.490 NanoFolder: 0.316 Sensitivity Multilign(20): 0.419 NanoFolder: 0.324 Positive Predictive Value Multilign(20): 0.579 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.524 NanoFolder: 0.490 Sensitivity RNAwolf: 0.483 NanoFolder: 0.495 Positive Predictive Value RNAwolf: 0.578 NanoFolder: 0.494 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.24403703175e-08	4 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.403 NanoFolder: 0.280 Sensitivity Murlet(seed): 0.237 NanoFolder: 0.298 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	15 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.636 NanoFolder: 0.522 Sensitivity MCFold: 0.654 NanoFolder: 0.538 Positive Predictive Value MCFold: 0.624 NanoFolder: 0.515 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.45096400029e-08	16 NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.478 Vsfold5: 0.462 Sensitivity NanoFolder: 0.484 Vsfold5: 0.403 Positive Predictive Value NanoFolder: 0.482 Vsfold5: 0.539 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.98533417679e-07	8 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.561 RDfolder: 0.477 Sensitivity NanoFolder: 0.542 RDfolder: 0.392 Positive Predictive Value NanoFolder: 0.593 RDfolder: 0.594 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.346 RSpredict(seed): 0.090 Sensitivity NanoFolder: 0.353 RSpredict(seed): 0.038 Positive Predictive Value NanoFolder: 0.349 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.346 PPfold(seed): 0.125 Sensitivity NanoFolder: 0.353 PPfold(seed): 0.030 Positive Predictive Value NanoFolder: 0.349 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		? NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.346 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.353 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.349 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.403 NanoFolder: 0.395 Sensitivity Multilign(seed): 0.306 NanoFolder: 0.371 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.562 NanoFolder: 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.863 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.526 NanoFolder: 0.316 Sensitivity TurboFold(20): 0.419 NanoFolder: 0.324 Positive Predictive Value TurboFold(20): 0.667 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs CMfinder(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.627 NanoFolder: 0.316 Sensitivity PETfold_pre2.0(20): 0.507 NanoFolder: 0.324 Positive Predictive Value PETfold_pre2.0(20): 0.781 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.622 NanoFolder: 0.316 Sensitivity PPfold(20): 0.486 NanoFolder: 0.324 Positive Predictive Value PPfold(20): 0.800 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.341 Carnac(seed): 0.154 Sensitivity NanoFolder: 0.351 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.339 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	44 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.673 Mastr(seed): 0.263 Sensitivity MXScarna(seed): 0.562 Mastr(seed): 0.077 Positive Predictive Value MXScarna(seed): 0.809 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Mastr(seed): 0.264 Sensitivity CentroidFold: 0.545 Mastr(seed): 0.078 Positive Predictive Value CentroidFold: 0.719 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.680 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.520 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.892 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.644 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.491 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.849 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.477 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.844 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.605 Mastr(seed): 0.258 Sensitivity Sfold: 0.520 Mastr(seed): 0.075 Positive Predictive Value Sfold: 0.707 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.628 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.523 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.757 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	45 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.589 Mastr(seed): 0.258 Sensitivity Contrafold: 0.533 Mastr(seed): 0.075 Positive Predictive Value Contrafold: 0.655 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.625 Mastr(seed): 0.279 Sensitivity Fold: 0.569 Mastr(seed): 0.088 Positive Predictive Value Fold: 0.690 Mastr(seed): 0.886 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.598 Mastr(seed): 0.258 Sensitivity HotKnots: 0.543 Mastr(seed): 0.075 Positive Predictive Value HotKnots: 0.662 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.501 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	11 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.590 Mastr(seed): 0.000 Sensitivity IPknot: 0.471 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.62909925123e-09	40 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.605 Mastr(seed): 0.273 Sensitivity MaxExpect: 0.543 Mastr(seed): 0.083 Positive Predictive Value MaxExpect: 0.677 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.595 Mastr(seed): 0.258 Sensitivity UNAFold: 0.534 Mastr(seed): 0.075 Positive Predictive Value UNAFold: 0.667 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.616 Mastr(seed): 0.000 Sensitivity ContextFold: 0.476 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.801 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	45 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.591 Mastr(seed): 0.258 Sensitivity RNAshapes: 0.529 Mastr(seed): 0.075 Positive Predictive Value RNAshapes: 0.664 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.600 Mastr(seed): 0.258 Sensitivity RNAfold: 0.542 Mastr(seed): 0.075 Positive Predictive Value RNAfold: 0.667 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.600 Mastr(seed): 0.258 Sensitivity PknotsRG: 0.545 Mastr(seed): 0.075 Positive Predictive Value PknotsRG: 0.666 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.605 Mastr(seed): 0.264 Sensitivity CentroidAlifold(seed): 0.419 Mastr(seed): 0.078 Positive Predictive Value CentroidAlifold(seed): 0.878 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.570 Mastr(seed): 0.213 Sensitivity ProbKnot: 0.529 Mastr(seed): 0.046 Positive Predictive Value ProbKnot: 0.618 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.582 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.423 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.804 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.582 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.371 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.915 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	33 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.566 Mastr(seed): 0.304 Sensitivity Afold: 0.525 Mastr(seed): 0.103 Positive Predictive Value Afold: 0.614 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.560 Mastr(seed): 0.258 Sensitivity RNAsubopt: 0.511 Mastr(seed): 0.075 Positive Predictive Value RNAsubopt: 0.619 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.640 Mastr(seed): 0.263 Sensitivity Cylofold: 0.553 Mastr(seed): 0.070 Positive Predictive Value Cylofold: 0.747 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	45 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.556 Mastr(seed): 0.258 Sensitivity McQFold: 0.489 Mastr(seed): 0.075 Positive Predictive Value McQFold: 0.636 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Mastr(seed): 0.319 Sensitivity RNAalifold(seed): 0.397 Mastr(seed): 0.114 Positive Predictive Value RNAalifold(seed): 0.887 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.601 Mastr(seed): 0.279 Sensitivity Pknots: 0.547 Mastr(seed): 0.087 Positive Predictive Value Pknots: 0.666 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-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	17 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Mastr(seed): 0.483 Sensitivity RNASampler(seed): 0.535 Mastr(seed): 0.261 Positive Predictive Value RNASampler(seed): 0.851 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-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	27 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.547 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.428 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.702 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.525 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.346 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.800 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	45 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.509 Mastr(seed): 0.258 Sensitivity Vsfold4: 0.437 Mastr(seed): 0.075 Positive Predictive Value Vsfold4: 0.599 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.374 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.609 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.521 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.428 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.643 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.21563533328e-09	11 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.375 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.467 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	26 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 Mastr(seed): 0.365 Sensitivity Murlet(seed): 0.337 Mastr(seed): 0.149 Positive Predictive Value Murlet(seed): 0.868 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.502 Mastr(seed): 0.304 Sensitivity MCFold: 0.526 Mastr(seed): 0.104 Positive Predictive Value MCFold: 0.487 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.477 Mastr(seed): 0.258 Sensitivity Vsfold5: 0.413 Mastr(seed): 0.075 Positive Predictive Value Vsfold5: 0.555 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.556 Mastr(seed): 0.357 Sensitivity RDfolder: 0.462 Mastr(seed): 0.143 Positive Predictive Value RDfolder: 0.678 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.314 Mastr(seed): 0.263 Sensitivity RSpredict(seed): 0.161 Mastr(seed): 0.077 Positive Predictive Value RSpredict(seed): 0.620 Mastr(seed): 0.900 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.102 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.020 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	7 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.346 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.353 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.349 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		? 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	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.475 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.750 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.551 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.620 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.500 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.775 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.456 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.672 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.514 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.861 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.331 Carnac(seed): 0.260 Sensitivity Mastr(seed): 0.122 Carnac(seed): 0.068 Positive Predictive Value Mastr(seed): 0.900 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08
CMfinder(seed)	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 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 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 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 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 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 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 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 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 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 CMfinder(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value CMfinder(seed): N/A CentroidHomfold‑LAST: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 CRWrnafold Matthews Correlation Coefficient CMfinder(seed): N/A CRWrnafold: N/A Sensitivity CMfinder(seed): N/A CRWrnafold: N/A Positive Predictive Value CMfinder(seed): N/A CRWrnafold: 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 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 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 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 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 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 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 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 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 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 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 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 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		? 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	? 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	? 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	? 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_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	? 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	? 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	? 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
Multilign(seed)	5 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 MXScarna(seed): 0.575 Sensitivity Multilign(seed): 0.475 MXScarna(seed): 0.475 Positive Predictive Value Multilign(seed): 0.750 MXScarna(seed): 0.708 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Multilign(seed): 0.593 Sensitivity CentroidFold: 0.500 Multilign(seed): 0.475 Positive Predictive Value CentroidFold: 0.790 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.707 Multilign(seed): 0.678 Sensitivity CentroidAlifold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value CentroidAlifold(20): 0.926 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.678 RNAalifold(20): 0.672 Sensitivity Multilign(seed): 0.543 RNAalifold(20): 0.536 Positive Predictive Value Multilign(seed): 0.852 RNAalifold(20): 0.851 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.711 Multilign(seed): 0.678 Sensitivity RNASampler(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value RNASampler(20): 0.938 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.655 Multilign(seed): 0.593 Sensitivity Sfold: 0.532 Multilign(seed): 0.475 Positive Predictive Value Sfold: 0.816 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.678 MXScarna(20): 0.664 Sensitivity Multilign(seed): 0.543 MXScarna(20): 0.565 Positive Predictive Value Multilign(seed): 0.852 MXScarna(20): 0.788 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.606 Multilign(seed): 0.593 Sensitivity Contrafold: 0.506 Multilign(seed): 0.475 Positive Predictive Value Contrafold: 0.734 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.593 Fold: 0.572 Sensitivity Multilign(seed): 0.475 Fold: 0.481 Positive Predictive Value Multilign(seed): 0.750 Fold: 0.691 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.672 Multilign(seed): 0.593 Sensitivity HotKnots: 0.563 Multilign(seed): 0.475 Positive Predictive Value HotKnots: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.634 Multilign(seed): 0.593 Sensitivity CentroidHomfold‑LAST: 0.481 Multilign(seed): 0.475 Positive Predictive Value CentroidHomfold‑LAST: 0.844 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.560 Multilign(seed): 0.538 Sensitivity IPknot: 0.435 Multilign(seed): 0.420 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.593 MaxExpect: 0.575 Sensitivity Multilign(seed): 0.475 MaxExpect: 0.481 Positive Predictive Value Multilign(seed): 0.750 MaxExpect: 0.697 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.593 UNAFold: 0.590 Sensitivity Multilign(seed): 0.475 UNAFold: 0.494 Positive Predictive Value Multilign(seed): 0.750 UNAFold: 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.532 Multilign(seed): 0.403 Sensitivity ContextFold: 0.435 Multilign(seed): 0.306 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.672 Multilign(seed): 0.593 Sensitivity RNAshapes: 0.563 Multilign(seed): 0.475 Positive Predictive Value RNAshapes: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.672 Multilign(seed): 0.593 Sensitivity RNAfold: 0.563 Multilign(seed): 0.475 Positive Predictive Value RNAfold: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.667 Multilign(seed): 0.593 Sensitivity PknotsRG: 0.557 Multilign(seed): 0.475 Positive Predictive Value PknotsRG: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.657 Multilign(seed): 0.593 Sensitivity CentroidAlifold(seed): 0.481 Multilign(seed): 0.475 Positive Predictive Value CentroidAlifold(seed): 0.905 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.593 ProbKnot: 0.562 Sensitivity Multilign(seed): 0.475 ProbKnot: 0.481 Positive Predictive Value Multilign(seed): 0.750 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Murlet(20): 0.667 Sensitivity Multilign(seed): 0.543 Murlet(20): 0.529 Positive Predictive Value Multilign(seed): 0.852 Murlet(20): 0.849 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Carnac(20): 0.566 Sensitivity Multilign(seed): 0.543 Carnac(20): 0.362 Positive Predictive Value Multilign(seed): 0.852 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.781 Multilign(seed): 0.610 Sensitivity Afold: 0.676 Multilign(seed): 0.500 Positive Predictive Value Afold: 0.909 Multilign(seed): 0.755 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.593 RNAsubopt: 0.588 Sensitivity Multilign(seed): 0.475 RNAsubopt: 0.494 Positive Predictive Value Multilign(seed): 0.750 RNAsubopt: 0.709 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.633 Multilign(seed): 0.593 Sensitivity Cylofold: 0.519 Multilign(seed): 0.475 Positive Predictive Value Cylofold: 0.781 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.672 Multilign(seed): 0.593 Sensitivity McQFold: 0.563 Multilign(seed): 0.475 Positive Predictive Value McQFold: 0.809 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 RNAalifold(seed): 0.550 Sensitivity Multilign(seed): 0.475 RNAalifold(seed): 0.399 Positive Predictive Value Multilign(seed): 0.750 RNAalifold(seed): 0.768 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.607 Multilign(seed): 0.593 Sensitivity Pknots: 0.519 Multilign(seed): 0.475 Positive Predictive Value Pknots: 0.719 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 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	4 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.588 RNASampler(seed): 0.564 Sensitivity Multilign(seed): 0.483 RNASampler(seed): 0.405 Positive Predictive Value Multilign(seed): 0.727 RNASampler(seed): 0.797 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	4 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.678 RSpredict(20): 0.583 Sensitivity Multilign(seed): 0.543 RSpredict(20): 0.449 Positive Predictive Value Multilign(seed): 0.852 RSpredict(20): 0.765 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.678 Mastr(20): 0.611 Sensitivity Multilign(seed): 0.543 Mastr(20): 0.471 Positive Predictive Value Multilign(seed): 0.852 Mastr(20): 0.802 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.593 Vsfold4: 0.445 Sensitivity Multilign(seed): 0.475 Vsfold4: 0.367 Positive Predictive Value Multilign(seed): 0.750 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.403 RNASLOpt: 0.332 Sensitivity Multilign(seed): 0.306 RNASLOpt: 0.242 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 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	4 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.538 RNAwolf: 0.466 Sensitivity Multilign(seed): 0.420 RNAwolf: 0.413 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Murlet(seed): 0.447 Sensitivity Multilign(seed): 0.475 Murlet(seed): 0.285 Positive Predictive Value Multilign(seed): 0.750 Murlet(seed): 0.714 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.588 MCFold: 0.558 Sensitivity Multilign(seed): 0.483 MCFold: 0.552 Positive Predictive Value Multilign(seed): 0.727 MCFold: 0.577 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.593 Vsfold5: 0.380 Sensitivity Multilign(seed): 0.475 Vsfold5: 0.316 Positive Predictive Value Multilign(seed): 0.750 Vsfold5: 0.472 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.593 RDfolder: 0.476 Sensitivity Multilign(seed): 0.475 RDfolder: 0.361 Positive Predictive Value Multilign(seed): 0.750 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 RSpredict(seed): 0.364 Sensitivity Multilign(seed): 0.475 RSpredict(seed): 0.215 Positive Predictive Value Multilign(seed): 0.750 RSpredict(seed): 0.630 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 PPfold(seed): 0.179 Sensitivity Multilign(seed): 0.420 PPfold(seed): 0.043 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.403 NanoFolder: 0.395 Sensitivity Multilign(seed): 0.306 NanoFolder: 0.371 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.475 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.750 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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		? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.623 Multilign(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.484 Multilign(seed): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.678 Multilign(seed): 0.678 Sensitivity TurboFold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value TurboFold(20): 0.852 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 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	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Multilign(seed): 0.609 Sensitivity PETfold_pre2.0(20): 0.595 Multilign(seed): 0.452 Positive Predictive Value PETfold_pre2.0(20): 0.926 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 TurboFold(seed): 0.584 Sensitivity Multilign(seed): 0.475 TurboFold(seed): 0.475 Positive Predictive Value Multilign(seed): 0.750 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.703 Multilign(seed): 0.678 Sensitivity PPfold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value PPfold(20): 0.915 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Carnac(seed): 0.380 Sensitivity Multilign(seed): 0.475 Carnac(seed): 0.146 Positive Predictive Value Multilign(seed): 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(seed)	8 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MXScarna(seed): 0.586 Sensitivity PETfold_pre2.0(seed): 0.551 MXScarna(seed): 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidFold: 0.540 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidFold: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 CentroidAlifold(20): 0.650 Sensitivity PETfold_pre2.0(seed): 0.557 CentroidAlifold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.898 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.557 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(seed): 0.557 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Sfold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 Sfold: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(seed): 0.557 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.551 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Contrafold: 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Fold: 0.465 Sensitivity PETfold_pre2.0(seed): 0.551 Fold: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Fold: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 HotKnots: 0.518 Sensitivity PETfold_pre2.0(seed): 0.551 HotKnots: 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 HotKnots: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidHomfold‑LAST: 0.575 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidHomfold‑LAST: 0.453 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidHomfold‑LAST: 0.737 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 IPknot: 0.551 Sensitivity PETfold_pre2.0(seed): 0.551 IPknot: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MaxExpect: 0.458 Sensitivity PETfold_pre2.0(seed): 0.551 MaxExpect: 0.390 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 UNAFold: 0.413 Sensitivity PETfold_pre2.0(seed): 0.551 UNAFold: 0.358 Positive Predictive Value PETfold_pre2.0(seed): 0.843 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ContextFold: 0.616 Sensitivity PETfold_pre2.0(seed): 0.551 ContextFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ContextFold: 0.801 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAshapes: 0.476 Sensitivity PETfold_pre2.0(seed): 0.551 RNAshapes: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAshapes: 0.562 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAfold: 0.515 Sensitivity PETfold_pre2.0(seed): 0.551 RNAfold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PknotsRG: 0.569 Sensitivity PETfold_pre2.0(seed): 0.551 PknotsRG: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidAlifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidAlifold(seed): 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ProbKnot: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 ProbKnot: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.557 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(seed): 0.557 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 Afold: 0.389 Sensitivity PETfold_pre2.0(seed): 0.403 Afold: 0.375 Positive Predictive Value PETfold_pre2.0(seed): 0.644 Afold: 0.409 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAsubopt: 0.431 Sensitivity PETfold_pre2.0(seed): 0.551 RNAsubopt: 0.378 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAsubopt: 0.500 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Cylofold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.521 Cylofold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.821 Cylofold: 0.735 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 McQFold: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 McQFold: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 McQFold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 RNAalifold(seed): 0.472 Sensitivity PETfold_pre2.0(seed): 0.459 RNAalifold(seed): 0.293 Positive Predictive Value PETfold_pre2.0(seed): 0.726 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Pknots: 0.452 Sensitivity PETfold_pre2.0(seed): 0.551 Pknots: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Pknots: 0.518 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	2 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 RNASampler(seed): 0.198 Sensitivity PETfold_pre2.0(seed): 0.396 RNASampler(seed): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.656 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 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	5 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(seed): 0.557 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(seed): 0.557 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold4: 0.437 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold4: 0.350 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold4: 0.553 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNASLOpt: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 RNASLOpt: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(seed): 0.557 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAwolf: 0.339 Sensitivity PETfold_pre2.0(seed): 0.551 RNAwolf: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAwolf: 0.384 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 Murlet(seed): 0.425 Sensitivity PETfold_pre2.0(seed): 0.459 Murlet(seed): 0.248 Positive Predictive Value PETfold_pre2.0(seed): 0.726 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.663 MCFold: 0.441 Sensitivity PETfold_pre2.0(seed): 0.549 MCFold: 0.469 Positive Predictive Value PETfold_pre2.0(seed): 0.807 MCFold: 0.423 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold5: 0.372 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold5: 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold5: 0.443 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.634 RDfolder: 0.281 Sensitivity PETfold_pre2.0(seed): 0.515 RDfolder: 0.215 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RSpredict(seed): 0.110 Sensitivity PETfold_pre2.0(seed): 0.551 RSpredict(seed): 0.047 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PPfold(seed): 0.121 Sensitivity PETfold_pre2.0(seed): 0.551 PPfold(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.562 NanoFolder: 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.863 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.551 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	2 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.623 Multilign(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.484 Multilign(seed): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(seed): 0.557 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.830 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(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_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PETfold_pre2.0(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.557 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 TurboFold(seed): 0.460 Sensitivity PETfold_pre2.0(seed): 0.529 TurboFold(seed): 0.380 Positive Predictive Value PETfold_pre2.0(seed): 0.805 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(seed): 0.557 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Carnac(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.529 Carnac(seed): 0.021 Positive Predictive Value PETfold_pre2.0(seed): 0.805 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
TurboFold(20)	9 MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.634 TurboFold(20): 0.620 Sensitivity MXScarna(seed): 0.514 TurboFold(20): 0.500 Positive Predictive Value MXScarna(seed): 0.788 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.620 CentroidFold: 0.603 Sensitivity TurboFold(20): 0.500 CentroidFold: 0.500 Positive Predictive Value TurboFold(20): 0.775 CentroidFold: 0.732 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 TurboFold(20): 0.620 Sensitivity CentroidAlifold(20): 0.517 TurboFold(20): 0.500 Positive Predictive Value CentroidAlifold(20): 0.909 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.620 RNAalifold(20): 0.619 Sensitivity TurboFold(20): 0.500 RNAalifold(20): 0.483 Positive Predictive Value TurboFold(20): 0.775 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.660 TurboFold(20): 0.620 Sensitivity RNASampler(20): 0.507 TurboFold(20): 0.500 Positive Predictive Value RNASampler(20): 0.865 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.620 Sfold: 0.610 Sensitivity TurboFold(20): 0.500 Sfold: 0.500 Positive Predictive Value TurboFold(20): 0.775 Sfold: 0.751 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.620 MXScarna(20): 0.598 Sensitivity TurboFold(20): 0.500 MXScarna(20): 0.490 Positive Predictive Value TurboFold(20): 0.775 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.620 Contrafold: 0.589 Sensitivity TurboFold(20): 0.500 Contrafold: 0.507 Positive Predictive Value TurboFold(20): 0.775 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.620 Fold: 0.546 Sensitivity TurboFold(20): 0.500 Fold: 0.476 Positive Predictive Value TurboFold(20): 0.775 Fold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.636 TurboFold(20): 0.620 Sensitivity HotKnots: 0.555 TurboFold(20): 0.500 Positive Predictive Value HotKnots: 0.735 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 TurboFold(20): 0.620 Sensitivity CentroidHomfold‑LAST: 0.524 TurboFold(20): 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.822 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.594 IPknot: 0.571 Sensitivity TurboFold(20): 0.470 IPknot: 0.463 Positive Predictive Value TurboFold(20): 0.756 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.620 MaxExpect: 0.577 Sensitivity TurboFold(20): 0.500 MaxExpect: 0.497 Positive Predictive Value TurboFold(20): 0.775 MaxExpect: 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.620 UNAFold: 0.589 Sensitivity TurboFold(20): 0.500 UNAFold: 0.507 Positive Predictive Value TurboFold(20): 0.775 UNAFold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.579 TurboFold(20): 0.542 Sensitivity ContextFold: 0.443 TurboFold(20): 0.425 Positive Predictive Value ContextFold: 0.763 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.620 RNAshapes: 0.587 Sensitivity TurboFold(20): 0.500 RNAshapes: 0.503 Positive Predictive Value TurboFold(20): 0.775 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.620 RNAfold: 0.587 Sensitivity TurboFold(20): 0.500 RNAfold: 0.507 Positive Predictive Value TurboFold(20): 0.775 RNAfold: 0.687 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.628 TurboFold(20): 0.620 Sensitivity PknotsRG: 0.552 TurboFold(20): 0.500 Positive Predictive Value PknotsRG: 0.721 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.624 TurboFold(20): 0.620 Sensitivity CentroidAlifold(seed): 0.421 TurboFold(20): 0.500 Positive Predictive Value CentroidAlifold(seed): 0.931 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.620 ProbKnot: 0.574 Sensitivity TurboFold(20): 0.500 ProbKnot: 0.514 Positive Predictive Value TurboFold(20): 0.775 ProbKnot: 0.648 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Murlet(20): 0.576 Sensitivity TurboFold(20): 0.500 Murlet(20): 0.438 Positive Predictive Value TurboFold(20): 0.775 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Carnac(20): 0.540 Sensitivity TurboFold(20): 0.500 Carnac(20): 0.341 Positive Predictive Value TurboFold(20): 0.775 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.593 Afold: 0.564 Sensitivity TurboFold(20): 0.491 Afold: 0.519 Positive Predictive Value TurboFold(20): 0.722 Afold: 0.618 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.620 RNAsubopt: 0.583 Sensitivity TurboFold(20): 0.500 RNAsubopt: 0.507 Positive Predictive Value TurboFold(20): 0.775 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.689 TurboFold(20): 0.679 Sensitivity Cylofold: 0.576 TurboFold(20): 0.537 Positive Predictive Value Cylofold: 0.830 TurboFold(20): 0.865 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.620 McQFold: 0.560 Sensitivity TurboFold(20): 0.500 McQFold: 0.486 Positive Predictive Value TurboFold(20): 0.775 McQFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 TurboFold(20): 0.590 Sensitivity RNAalifold(seed): 0.383 TurboFold(20): 0.469 Positive Predictive Value RNAalifold(seed): 0.920 TurboFold(20): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.620 Pknots: 0.537 Sensitivity TurboFold(20): 0.500 Pknots: 0.472 Positive Predictive Value TurboFold(20): 0.775 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.582 RNASampler(seed): 0.581 Sensitivity TurboFold(20): 0.488 RNASampler(seed): 0.426 Positive Predictive Value TurboFold(20): 0.700 RNASampler(seed): 0.797 Number of pairs reference - predicted secondary structure: 4 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	9 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.620 RSpredict(20): 0.494 Sensitivity TurboFold(20): 0.500 RSpredict(20): 0.376 Positive Predictive Value TurboFold(20): 0.775 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Mastr(20): 0.592 Sensitivity TurboFold(20): 0.500 Mastr(20): 0.417 Positive Predictive Value TurboFold(20): 0.775 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.620 Vsfold4: 0.474 Sensitivity TurboFold(20): 0.500 Vsfold4: 0.390 Positive Predictive Value TurboFold(20): 0.775 Vsfold4: 0.585 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.542 RNASLOpt: 0.467 Sensitivity TurboFold(20): 0.425 RNASLOpt: 0.383 Positive Predictive Value TurboFold(20): 0.696 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.620 Multilign(20): 0.574 Sensitivity TurboFold(20): 0.500 Multilign(20): 0.490 Positive Predictive Value TurboFold(20): 0.775 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.594 RNAwolf: 0.364 Sensitivity TurboFold(20): 0.470 RNAwolf: 0.333 Positive Predictive Value TurboFold(20): 0.756 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.590 Murlet(seed): 0.527 Sensitivity TurboFold(20): 0.469 Murlet(seed): 0.306 Positive Predictive Value TurboFold(20): 0.748 Murlet(seed): 0.914 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.630 MCFold: 0.498 Sensitivity TurboFold(20): 0.516 MCFold: 0.512 Positive Predictive Value TurboFold(20): 0.776 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.620 Vsfold5: 0.461 Sensitivity TurboFold(20): 0.500 Vsfold5: 0.400 Positive Predictive Value TurboFold(20): 0.775 Vsfold5: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.679 RDfolder: 0.478 Sensitivity TurboFold(20): 0.537 RDfolder: 0.360 Positive Predictive Value TurboFold(20): 0.865 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.620 RSpredict(seed): 0.299 Sensitivity TurboFold(20): 0.500 RSpredict(seed): 0.138 Positive Predictive Value TurboFold(20): 0.775 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 PPfold(seed): 0.026 Sensitivity TurboFold(20): 0.470 PPfold(seed): 0.004 Positive Predictive Value TurboFold(20): 0.756 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.526 NanoFolder: 0.316 Sensitivity TurboFold(20): 0.419 NanoFolder: 0.324 Positive Predictive Value TurboFold(20): 0.667 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.620 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.500 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.775 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.678 Multilign(seed): 0.678 Sensitivity TurboFold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value TurboFold(20): 0.852 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(seed): 0.557 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.830 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.611 TurboFold(seed): 0.595 Sensitivity TurboFold(20): 0.490 TurboFold(seed): 0.490 Positive Predictive Value TurboFold(20): 0.768 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.663 TurboFold(20): 0.620 Sensitivity PPfold(20): 0.514 TurboFold(20): 0.500 Positive Predictive Value PPfold(20): 0.861 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.611 Carnac(seed): 0.268 Sensitivity TurboFold(20): 0.490 Carnac(seed): 0.072 Positive Predictive Value TurboFold(20): 0.768 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
CMfinder(20)	0 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: 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	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 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	0 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(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(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): 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 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	0 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): 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 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	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(20)	5 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(seed): 0.593 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(seed): 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(seed): 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidFold: 0.517 Sensitivity PETfold_pre2.0(20): 0.497 CentroidFold: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 PETfold_pre2.0(20): 0.625 Sensitivity CentroidAlifold(20): 0.473 PETfold_pre2.0(20): 0.497 Positive Predictive Value CentroidAlifold(20): 0.898 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.497 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(20): 0.497 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Sfold: 0.507 Sensitivity PETfold_pre2.0(20): 0.497 Sfold: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Contrafold: 0.511 Sensitivity PETfold_pre2.0(20): 0.497 Contrafold: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.790 Contrafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Fold: 0.429 Sensitivity PETfold_pre2.0(20): 0.497 Fold: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.790 Fold: 0.496 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 HotKnots: 0.561 Sensitivity PETfold_pre2.0(20): 0.497 HotKnots: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 HotKnots: 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidHomfold‑LAST: 0.581 Sensitivity PETfold_pre2.0(20): 0.497 CentroidHomfold‑LAST: 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidHomfold‑LAST: 0.729 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 IPknot: 0.502 Sensitivity PETfold_pre2.0(20): 0.497 IPknot: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MaxExpect: 0.479 Sensitivity PETfold_pre2.0(20): 0.497 MaxExpect: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 UNAFold: 0.478 Sensitivity PETfold_pre2.0(20): 0.497 UNAFold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 UNAFold: 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ContextFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.497 ContextFold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAshapes: 0.475 Sensitivity PETfold_pre2.0(20): 0.497 RNAshapes: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAshapes: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAfold: 0.476 Sensitivity PETfold_pre2.0(20): 0.497 RNAfold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(20): 0.497 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 PknotsRG: 0.618 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidAlifold(seed): 0.613 Sensitivity PETfold_pre2.0(20): 0.497 CentroidAlifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ProbKnot: 0.488 Sensitivity PETfold_pre2.0(20): 0.497 ProbKnot: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ProbKnot: 0.544 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.497 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(20): 0.790 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.333 Afold: 0.311 Sensitivity PETfold_pre2.0(20): 0.250 Afold: 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.320 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAsubopt: 0.477 Sensitivity PETfold_pre2.0(20): 0.497 RNAsubopt: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAsubopt: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 Cylofold: 0.620 Sensitivity PETfold_pre2.0(20): 0.513 Cylofold: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.872 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 McQFold: 0.409 Sensitivity PETfold_pre2.0(20): 0.497 McQFold: 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.790 McQFold: 0.466 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.586 PETfold_pre2.0(20): 0.527 Sensitivity RNAalifold(seed): 0.345 PETfold_pre2.0(20): 0.407 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Pknots: 0.371 Sensitivity PETfold_pre2.0(20): 0.497 Pknots: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Pknots: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	1 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.310 PETfold_pre2.0(20): 0.193 Sensitivity RNASampler(seed): 0.242 PETfold_pre2.0(20): 0.152 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 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	5 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold4: 0.401 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold4: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold4: 0.505 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASLOpt: 0.467 Sensitivity PETfold_pre2.0(20): 0.497 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(20): 0.497 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAwolf: 0.220 Sensitivity PETfold_pre2.0(20): 0.497 RNAwolf: 0.204 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAwolf: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.539 PETfold_pre2.0(20): 0.527 Sensitivity Murlet(seed): 0.292 PETfold_pre2.0(20): 0.407 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.586 MCFold: 0.444 Sensitivity PETfold_pre2.0(20): 0.464 MCFold: 0.472 Positive Predictive Value PETfold_pre2.0(20): 0.744 MCFold: 0.424 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold5: 0.384 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold5: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold5: 0.448 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 RDfolder: 0.387 Sensitivity PETfold_pre2.0(20): 0.513 RDfolder: 0.288 Positive Predictive Value PETfold_pre2.0(20): 0.872 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(seed): 0.184 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(seed): 0.072 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(seed): 0.034 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(seed): 0.006 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.627 NanoFolder: 0.316 Sensitivity PETfold_pre2.0(20): 0.507 NanoFolder: 0.324 Positive Predictive Value PETfold_pre2.0(20): 0.781 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	1 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Multilign(seed): 0.609 Sensitivity PETfold_pre2.0(20): 0.595 Multilign(seed): 0.452 Positive Predictive Value PETfold_pre2.0(20): 0.926 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PETfold_pre2.0(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.557 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(seed): 0.519 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(seed): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(seed): 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(seed)	9 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.573 TurboFold(seed): 0.550 Sensitivity MXScarna(seed): 0.459 TurboFold(seed): 0.456 Positive Predictive Value MXScarna(seed): 0.722 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.585 TurboFold(seed): 0.550 Sensitivity CentroidFold: 0.481 TurboFold(seed): 0.456 Positive Predictive Value CentroidFold: 0.720 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.664 TurboFold(seed): 0.595 Sensitivity CentroidAlifold(20): 0.494 TurboFold(seed): 0.490 Positive Predictive Value CentroidAlifold(20): 0.897 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 RNAalifold(20): 0.592 Sensitivity TurboFold(seed): 0.490 RNAalifold(20): 0.456 Positive Predictive Value TurboFold(seed): 0.729 RNAalifold(20): 0.774 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.642 TurboFold(seed): 0.595 Sensitivity RNASampler(20): 0.487 TurboFold(seed): 0.490 Positive Predictive Value RNASampler(20): 0.853 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.590 TurboFold(seed): 0.550 Sensitivity Sfold: 0.481 TurboFold(seed): 0.456 Positive Predictive Value Sfold: 0.731 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 MXScarna(20): 0.569 Sensitivity TurboFold(seed): 0.490 MXScarna(20): 0.464 Positive Predictive Value TurboFold(seed): 0.729 MXScarna(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.573 TurboFold(seed): 0.550 Sensitivity Contrafold: 0.488 TurboFold(seed): 0.456 Positive Predictive Value Contrafold: 0.680 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.550 Fold: 0.497 Sensitivity TurboFold(seed): 0.456 Fold: 0.431 Positive Predictive Value TurboFold(seed): 0.672 Fold: 0.581 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.628 TurboFold(seed): 0.550 Sensitivity HotKnots: 0.551 TurboFold(seed): 0.456 Positive Predictive Value HotKnots: 0.722 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.593 TurboFold(seed): 0.550 Sensitivity CentroidHomfold‑LAST: 0.470 TurboFold(seed): 0.456 Positive Predictive Value CentroidHomfold‑LAST: 0.756 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.544 TurboFold(seed): 0.517 Sensitivity IPknot: 0.437 TurboFold(seed): 0.422 Positive Predictive Value IPknot: 0.685 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.550 MaxExpect: 0.528 Sensitivity TurboFold(seed): 0.456 MaxExpect: 0.452 Positive Predictive Value TurboFold(seed): 0.672 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.550 UNAFold: 0.535 Sensitivity TurboFold(seed): 0.456 UNAFold: 0.463 Positive Predictive Value TurboFold(seed): 0.672 UNAFold: 0.627 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.576 TurboFold(seed): 0.460 Sensitivity ContextFold: 0.449 TurboFold(seed): 0.380 Positive Predictive Value ContextFold: 0.743 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.578 TurboFold(seed): 0.550 Sensitivity RNAshapes: 0.498 TurboFold(seed): 0.456 Positive Predictive Value RNAshapes: 0.678 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.578 TurboFold(seed): 0.550 Sensitivity RNAfold: 0.502 TurboFold(seed): 0.456 Positive Predictive Value RNAfold: 0.673 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.621 TurboFold(seed): 0.550 Sensitivity PknotsRG: 0.548 TurboFold(seed): 0.456 Positive Predictive Value PknotsRG: 0.711 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.615 TurboFold(seed): 0.550 Sensitivity CentroidAlifold(seed): 0.410 TurboFold(seed): 0.456 Positive Predictive Value CentroidAlifold(seed): 0.928 TurboFold(seed): 0.672 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.550 ProbKnot: 0.526 Sensitivity TurboFold(seed): 0.456 ProbKnot: 0.470 Positive Predictive Value TurboFold(seed): 0.672 ProbKnot: 0.596 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Murlet(20): 0.554 Sensitivity TurboFold(seed): 0.490 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.729 Murlet(20): 0.747 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Carnac(20): 0.523 Sensitivity TurboFold(seed): 0.490 Carnac(20): 0.316 Positive Predictive Value TurboFold(seed): 0.729 Carnac(20): 0.874 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	9 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.550 RNAsubopt: 0.530 Sensitivity TurboFold(seed): 0.456 RNAsubopt: 0.463 Positive Predictive Value TurboFold(seed): 0.672 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.683 TurboFold(seed): 0.598 Sensitivity Cylofold: 0.571 TurboFold(seed): 0.474 Positive Predictive Value Cylofold: 0.824 TurboFold(seed): 0.762 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.550 McQFold: 0.548 Sensitivity TurboFold(seed): 0.456 McQFold: 0.481 Positive Predictive Value TurboFold(seed): 0.672 McQFold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.529 TurboFold(seed): 0.517 Sensitivity RNAalifold(seed): 0.349 TurboFold(seed): 0.428 Positive Predictive Value RNAalifold(seed): 0.808 TurboFold(seed): 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.550 Pknots: 0.526 Sensitivity TurboFold(seed): 0.456 Pknots: 0.466 Positive Predictive Value TurboFold(seed): 0.672 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	5 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.504 TurboFold(seed): 0.480 Sensitivity RNASampler(seed): 0.369 TurboFold(seed): 0.423 Positive Predictive Value RNASampler(seed): 0.696 TurboFold(seed): 0.553 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	8 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 RSpredict(20): 0.484 Sensitivity TurboFold(seed): 0.490 RSpredict(20): 0.373 Positive Predictive Value TurboFold(seed): 0.729 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.595 Mastr(20): 0.572 Sensitivity TurboFold(seed): 0.490 Mastr(20): 0.399 Positive Predictive Value TurboFold(seed): 0.729 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	6 RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 TurboFold(seed): 0.460 Sensitivity RNASLOpt: 0.380 TurboFold(seed): 0.380 Positive Predictive Value RNASLOpt: 0.582 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	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	8 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAwolf: 0.344 Sensitivity TurboFold(seed): 0.422 RNAwolf: 0.316 Positive Predictive Value TurboFold(seed): 0.642 RNAwolf: 0.384 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Murlet(seed): 0.465 Sensitivity TurboFold(seed): 0.428 Murlet(seed): 0.279 Positive Predictive Value TurboFold(seed): 0.632 Murlet(seed): 0.780 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.550 MCFold: 0.497 Sensitivity TurboFold(seed): 0.465 MCFold: 0.510 Positive Predictive Value TurboFold(seed): 0.659 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.550 Vsfold5: 0.409 Sensitivity TurboFold(seed): 0.456 Vsfold5: 0.353 Positive Predictive Value TurboFold(seed): 0.672 Vsfold5: 0.483 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	9 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 RSpredict(seed): 0.278 Sensitivity TurboFold(seed): 0.456 RSpredict(seed): 0.141 Positive Predictive Value TurboFold(seed): 0.672 RSpredict(seed): 0.556 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 PPfold(seed): 0.118 Sensitivity TurboFold(seed): 0.422 PPfold(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.642 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	9 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.456 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.672 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	5 Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 TurboFold(seed): 0.584 Sensitivity Multilign(seed): 0.475 TurboFold(seed): 0.475 Positive Predictive Value Multilign(seed): 0.750 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 TurboFold(seed): 0.460 Sensitivity PETfold_pre2.0(seed): 0.529 TurboFold(seed): 0.380 Positive Predictive Value PETfold_pre2.0(seed): 0.805 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.611 TurboFold(seed): 0.595 Sensitivity TurboFold(20): 0.490 TurboFold(seed): 0.490 Positive Predictive Value TurboFold(20): 0.768 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 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	5 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(seed): 0.519 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(seed): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(seed): 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.641 TurboFold(seed): 0.595 Sensitivity PPfold(20): 0.490 TurboFold(seed): 0.490 Positive Predictive Value PPfold(20): 0.843 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 Carnac(seed): 0.284 Sensitivity TurboFold(seed): 0.456 Carnac(seed): 0.081 Positive Predictive Value TurboFold(seed): 0.672 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	9 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(seed): 0.634 Sensitivity PPfold(20): 0.514 MXScarna(seed): 0.514 Positive Predictive Value PPfold(20): 0.861 MXScarna(seed): 0.788 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.663 CentroidFold: 0.603 Sensitivity PPfold(20): 0.514 CentroidFold: 0.500 Positive Predictive Value PPfold(20): 0.861 CentroidFold: 0.732 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 PPfold(20): 0.663 Sensitivity CentroidAlifold(20): 0.517 PPfold(20): 0.514 Positive Predictive Value CentroidAlifold(20): 0.909 PPfold(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNAalifold(20): 0.619 Sensitivity PPfold(20): 0.514 RNAalifold(20): 0.483 Positive Predictive Value PPfold(20): 0.861 RNAalifold(20): 0.800 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNASampler(20): 0.660 Sensitivity PPfold(20): 0.514 RNASampler(20): 0.507 Positive Predictive Value PPfold(20): 0.861 RNASampler(20): 0.865 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.663 Sfold: 0.610 Sensitivity PPfold(20): 0.514 Sfold: 0.500 Positive Predictive Value PPfold(20): 0.861 Sfold: 0.751 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(20): 0.598 Sensitivity PPfold(20): 0.514 MXScarna(20): 0.490 Positive Predictive Value PPfold(20): 0.861 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.663 Contrafold: 0.589 Sensitivity PPfold(20): 0.514 Contrafold: 0.507 Positive Predictive Value PPfold(20): 0.861 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.663 Fold: 0.546 Sensitivity PPfold(20): 0.514 Fold: 0.476 Positive Predictive Value PPfold(20): 0.861 Fold: 0.633 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.663 HotKnots: 0.636 Sensitivity PPfold(20): 0.514 HotKnots: 0.555 Positive Predictive Value PPfold(20): 0.861 HotKnots: 0.735 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.663 CentroidHomfold‑LAST: 0.654 Sensitivity PPfold(20): 0.514 CentroidHomfold‑LAST: 0.524 Positive Predictive Value PPfold(20): 0.861 CentroidHomfold‑LAST: 0.822 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.665 IPknot: 0.571 Sensitivity PPfold(20): 0.519 IPknot: 0.463 Positive Predictive Value PPfold(20): 0.859 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.663 MaxExpect: 0.577 Sensitivity PPfold(20): 0.514 MaxExpect: 0.497 Positive Predictive Value PPfold(20): 0.861 MaxExpect: 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.663 UNAFold: 0.589 Sensitivity PPfold(20): 0.514 UNAFold: 0.507 Positive Predictive Value PPfold(20): 0.861 UNAFold: 0.690 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.616 ContextFold: 0.579 Sensitivity PPfold(20): 0.473 ContextFold: 0.443 Positive Predictive Value PPfold(20): 0.806 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.663 RNAshapes: 0.587 Sensitivity PPfold(20): 0.514 RNAshapes: 0.503 Positive Predictive Value PPfold(20): 0.861 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.663 RNAfold: 0.587 Sensitivity PPfold(20): 0.514 RNAfold: 0.507 Positive Predictive Value PPfold(20): 0.861 RNAfold: 0.687 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.663 PknotsRG: 0.628 Sensitivity PPfold(20): 0.514 PknotsRG: 0.552 Positive Predictive Value PPfold(20): 0.861 PknotsRG: 0.721 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 CentroidAlifold(seed): 0.624 Sensitivity PPfold(20): 0.514 CentroidAlifold(seed): 0.421 Positive Predictive Value PPfold(20): 0.861 CentroidAlifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.663 ProbKnot: 0.574 Sensitivity PPfold(20): 0.514 ProbKnot: 0.514 Positive Predictive Value PPfold(20): 0.861 ProbKnot: 0.648 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.663 Murlet(20): 0.576 Sensitivity PPfold(20): 0.514 Murlet(20): 0.438 Positive Predictive Value PPfold(20): 0.861 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.663 Carnac(20): 0.540 Sensitivity PPfold(20): 0.514 Carnac(20): 0.341 Positive Predictive Value PPfold(20): 0.861 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Afold vs PPfold(20) Matthews Correlation Coefficient Afold: 0.564 PPfold(20): 0.522 Sensitivity Afold: 0.519 PPfold(20): 0.377 Positive Predictive Value Afold: 0.618 PPfold(20): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.663 RNAsubopt: 0.583 Sensitivity PPfold(20): 0.514 RNAsubopt: 0.507 Positive Predictive Value PPfold(20): 0.861 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.702 Cylofold: 0.689 Sensitivity PPfold(20): 0.542 Cylofold: 0.576 Positive Predictive Value PPfold(20): 0.917 Cylofold: 0.830 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.663 McQFold: 0.560 Sensitivity PPfold(20): 0.514 McQFold: 0.486 Positive Predictive Value PPfold(20): 0.861 McQFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.605 RNAalifold(seed): 0.591 Sensitivity PPfold(20): 0.455 RNAalifold(seed): 0.383 Positive Predictive Value PPfold(20): 0.812 RNAalifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.663 Pknots: 0.537 Sensitivity PPfold(20): 0.514 Pknots: 0.472 Positive Predictive Value PPfold(20): 0.861 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.581 PPfold(20): 0.569 Sensitivity RNASampler(seed): 0.426 PPfold(20): 0.426 Positive Predictive Value RNASampler(seed): 0.797 PPfold(20): 0.764 Number of pairs reference - predicted secondary structure: 4 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	9 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(20): 0.494 Sensitivity PPfold(20): 0.514 RSpredict(20): 0.376 Positive Predictive Value PPfold(20): 0.861 RSpredict(20): 0.657 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(20): 0.592 Sensitivity PPfold(20): 0.514 Mastr(20): 0.417 Positive Predictive Value PPfold(20): 0.861 Mastr(20): 0.846 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.663 Vsfold4: 0.474 Sensitivity PPfold(20): 0.514 Vsfold4: 0.390 Positive Predictive Value PPfold(20): 0.861 Vsfold4: 0.585 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.616 RNASLOpt: 0.467 Sensitivity PPfold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value PPfold(20): 0.806 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.663 Multilign(20): 0.574 Sensitivity PPfold(20): 0.514 Multilign(20): 0.490 Positive Predictive Value PPfold(20): 0.861 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.665 RNAwolf: 0.364 Sensitivity PPfold(20): 0.519 RNAwolf: 0.333 Positive Predictive Value PPfold(20): 0.859 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.605 Murlet(seed): 0.527 Sensitivity PPfold(20): 0.455 Murlet(seed): 0.306 Positive Predictive Value PPfold(20): 0.812 Murlet(seed): 0.914 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.650 MCFold: 0.498 Sensitivity PPfold(20): 0.500 MCFold: 0.512 Positive Predictive Value PPfold(20): 0.849 MCFold: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.663 Vsfold5: 0.461 Sensitivity PPfold(20): 0.514 Vsfold5: 0.400 Positive Predictive Value PPfold(20): 0.861 Vsfold5: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.702 RDfolder: 0.478 Sensitivity PPfold(20): 0.542 RDfolder: 0.360 Positive Predictive Value PPfold(20): 0.917 RDfolder: 0.646 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(seed): 0.299 Sensitivity PPfold(20): 0.514 RSpredict(seed): 0.138 Positive Predictive Value PPfold(20): 0.861 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 PPfold(seed): 0.026 Sensitivity PPfold(20): 0.519 PPfold(seed): 0.004 Positive Predictive Value PPfold(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.622 NanoFolder: 0.316 Sensitivity PPfold(20): 0.486 NanoFolder: 0.324 Positive Predictive Value PPfold(20): 0.800 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.514 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.861 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.703 Multilign(seed): 0.678 Sensitivity PPfold(20): 0.543 Multilign(seed): 0.543 Positive Predictive Value PPfold(20): 0.915 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(seed): 0.557 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.663 TurboFold(20): 0.620 Sensitivity PPfold(20): 0.514 TurboFold(20): 0.500 Positive Predictive Value PPfold(20): 0.861 TurboFold(20): 0.775 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.641 TurboFold(seed): 0.595 Sensitivity PPfold(20): 0.490 TurboFold(seed): 0.490 Positive Predictive Value PPfold(20): 0.843 TurboFold(seed): 0.729 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.641 Carnac(seed): 0.268 Sensitivity PPfold(20): 0.490 Carnac(seed): 0.072 Positive Predictive Value PPfold(20): 0.843 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Carnac(seed)	30 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.678 Carnac(seed): 0.260 Sensitivity MXScarna(seed): 0.575 Carnac(seed): 0.068 Positive Predictive Value MXScarna(seed): 0.803 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.668 Carnac(seed): 0.240 Sensitivity CentroidFold: 0.578 Carnac(seed): 0.058 Positive Predictive Value CentroidFold: 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	20 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.671 Carnac(seed): 0.160 Sensitivity CentroidAlifold(20): 0.510 Carnac(seed): 0.026 Positive Predictive Value CentroidAlifold(20): 0.887 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 Carnac(seed): 0.197 Sensitivity RNAalifold(20): 0.477 Carnac(seed): 0.039 Positive Predictive Value RNAalifold(20): 0.828 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 Carnac(seed): 0.197 Sensitivity RNASampler(20): 0.481 Carnac(seed): 0.039 Positive Predictive Value RNASampler(20): 0.849 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	30 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.684 Carnac(seed): 0.260 Sensitivity Sfold: 0.590 Carnac(seed): 0.068 Positive Predictive Value Sfold: 0.797 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.632 Carnac(seed): 0.197 Sensitivity MXScarna(20): 0.528 Carnac(seed): 0.039 Positive Predictive Value MXScarna(20): 0.761 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.649 Carnac(seed): 0.260 Sensitivity Contrafold: 0.583 Carnac(seed): 0.068 Positive Predictive Value Contrafold: 0.728 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.657 Carnac(seed): 0.275 Sensitivity Fold: 0.594 Carnac(seed): 0.076 Positive Predictive Value Fold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.678 Carnac(seed): 0.260 Sensitivity HotKnots: 0.612 Carnac(seed): 0.068 Positive Predictive Value HotKnots: 0.757 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.593 Carnac(seed): 0.284 Sensitivity CentroidHomfold‑LAST: 0.470 Carnac(seed): 0.081 Positive Predictive Value CentroidHomfold‑LAST: 0.756 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.544 Carnac(seed): 0.123 Sensitivity IPknot: 0.437 Carnac(seed): 0.015 Positive Predictive Value IPknot: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	28 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.643 Carnac(seed): 0.245 Sensitivity MaxExpect: 0.575 Carnac(seed): 0.061 Positive Predictive Value MaxExpect: 0.725 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.666 Carnac(seed): 0.260 Sensitivity UNAFold: 0.594 Carnac(seed): 0.068 Positive Predictive Value UNAFold: 0.752 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.576 Carnac(seed): 0.146 Sensitivity ContextFold: 0.449 Carnac(seed): 0.021 Positive Predictive Value ContextFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	30 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.679 Carnac(seed): 0.260 Sensitivity RNAshapes: 0.607 Carnac(seed): 0.068 Positive Predictive Value RNAshapes: 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.667 Carnac(seed): 0.260 Sensitivity RNAfold: 0.599 Carnac(seed): 0.068 Positive Predictive Value RNAfold: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.668 Carnac(seed): 0.260 Sensitivity PknotsRG: 0.604 Carnac(seed): 0.068 Positive Predictive Value PknotsRG: 0.745 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.674 Carnac(seed): 0.240 Sensitivity CentroidAlifold(seed): 0.511 Carnac(seed): 0.058 Positive Predictive Value CentroidAlifold(seed): 0.893 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.596 Carnac(seed): 0.189 Sensitivity ProbKnot: 0.545 Carnac(seed): 0.036 Positive Predictive Value ProbKnot: 0.658 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08	21 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.587 Carnac(seed): 0.197 Sensitivity Murlet(20): 0.425 Carnac(seed): 0.039 Positive Predictive Value Murlet(20): 0.817 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.583 Carnac(seed): 0.197 Sensitivity Carnac(20): 0.366 Carnac(seed): 0.039 Positive Predictive Value Carnac(20): 0.932 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.678 Carnac(seed): 0.311 Sensitivity Afold: 0.624 Carnac(seed): 0.097 Positive Predictive Value Afold: 0.742 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.636 Carnac(seed): 0.260 Sensitivity RNAsubopt: 0.575 Carnac(seed): 0.068 Positive Predictive Value RNAsubopt: 0.708 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.625 Carnac(seed): 0.212 Sensitivity Cylofold: 0.538 Carnac(seed): 0.045 Positive Predictive Value Cylofold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	30 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.618 Carnac(seed): 0.260 Sensitivity McQFold: 0.545 Carnac(seed): 0.068 Positive Predictive Value McQFold: 0.706 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Carnac(seed): 0.287 Sensitivity RNAalifold(seed): 0.460 Carnac(seed): 0.083 Positive Predictive Value RNAalifold(seed): 0.905 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.610 Carnac(seed): 0.260 Sensitivity Pknots: 0.563 Carnac(seed): 0.068 Positive Predictive Value Pknots: 0.666 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-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: 3.13260312532e-08	17 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.673 Carnac(seed): 0.379 Sensitivity RNASampler(seed): 0.535 Carnac(seed): 0.145 Positive Predictive Value RNASampler(seed): 0.851 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-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	21 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.514 Carnac(seed): 0.197 Sensitivity RSpredict(20): 0.394 Carnac(seed): 0.039 Positive Predictive Value RSpredict(20): 0.677 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.526 Carnac(seed): 0.197 Sensitivity Mastr(20): 0.357 Carnac(seed): 0.039 Positive Predictive Value Mastr(20): 0.780 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	30 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.531 Carnac(seed): 0.260 Sensitivity Vsfold4: 0.453 Carnac(seed): 0.068 Positive Predictive Value Vsfold4: 0.629 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 Carnac(seed): 0.146 Sensitivity RNASLOpt: 0.380 Carnac(seed): 0.021 Positive Predictive Value RNASLOpt: 0.582 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.511 Carnac(seed): 0.249 Sensitivity Multilign(20): 0.416 Carnac(seed): 0.062 Positive Predictive Value Multilign(20): 0.635 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.344 Carnac(seed): 0.123 Sensitivity RNAwolf: 0.316 Carnac(seed): 0.015 Positive Predictive Value RNAwolf: 0.384 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.539 Carnac(seed): 0.287 Sensitivity Murlet(seed): 0.337 Carnac(seed): 0.083 Positive Predictive Value Murlet(seed): 0.868 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.534 Carnac(seed): 0.273 Sensitivity MCFold: 0.554 Carnac(seed): 0.075 Positive Predictive Value MCFold: 0.521 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.503 Carnac(seed): 0.260 Sensitivity Vsfold5: 0.437 Carnac(seed): 0.068 Positive Predictive Value Vsfold5: 0.585 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.593 Carnac(seed): 0.351 Sensitivity RDfolder: 0.483 Carnac(seed): 0.125 Positive Predictive Value RDfolder: 0.737 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	30 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.404 Carnac(seed): 0.260 Sensitivity RSpredict(seed): 0.231 Carnac(seed): 0.068 Positive Predictive Value RSpredict(seed): 0.713 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.123 PPfold(seed): 0.118 Sensitivity Carnac(seed): 0.015 PPfold(seed): 0.027 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.341 Carnac(seed): 0.154 Sensitivity NanoFolder: 0.351 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.339 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.331 Carnac(seed): 0.260 Sensitivity Mastr(seed): 0.122 Carnac(seed): 0.068 Positive Predictive Value Mastr(seed): 0.900 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08	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	5 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.593 Carnac(seed): 0.380 Sensitivity Multilign(seed): 0.475 Carnac(seed): 0.146 Positive Predictive Value Multilign(seed): 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Carnac(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.529 Carnac(seed): 0.021 Positive Predictive Value PETfold_pre2.0(seed): 0.805 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.611 Carnac(seed): 0.268 Sensitivity TurboFold(20): 0.490 Carnac(seed): 0.072 Positive Predictive Value TurboFold(20): 0.768 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.550 Carnac(seed): 0.284 Sensitivity TurboFold(seed): 0.456 Carnac(seed): 0.081 Positive Predictive Value TurboFold(seed): 0.672 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.641 Carnac(seed): 0.268 Sensitivity PPfold(20): 0.490 Carnac(seed): 0.072 Positive Predictive Value PPfold(20): 0.843 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0

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