CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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All RNAs from the PDB dataset
standard base pair definition

	All RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. Standard base pair definition is used - it corresponds to the Leontis and Westhof classification i.e. the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry are considered as the secondary structure.
Updated: June 16, 2013
Base pair definition: standard
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Number of RNA sequences: 153
Robustness test: no

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

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

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

Summary of pairwise comparisons

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

Legend:

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

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

Detailed results of pairwise comparisons between methods

Legend:

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

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


CentroidAlifold(20)		- PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 CentroidAlifold(20): 0.798 Sensitivity PETfold_pre2.0(seed): 0.858 CentroidAlifold(20): 0.732 Positive Predictive Value PETfold_pre2.0(seed): 0.919 CentroidAlifold(20): 0.874 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.798 ContextFold: 0.748 Sensitivity CentroidAlifold(20): 0.732 ContextFold: 0.730 Positive Predictive Value CentroidAlifold(20): 0.874 ContextFold: 0.772 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 MXScarna(seed): 0.769 Sensitivity CentroidAlifold(20): 0.724 MXScarna(seed): 0.731 Positive Predictive Value CentroidAlifold(20): 0.903 MXScarna(seed): 0.814 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAalifold(20): 0.783 Sensitivity CentroidAlifold(20): 0.728 RNAalifold(20): 0.710 Positive Predictive Value CentroidAlifold(20): 0.901 RNAalifold(20): 0.867 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.798 PETfold_pre2.0(20): 0.793 Sensitivity CentroidAlifold(20): 0.732 PETfold_pre2.0(20): 0.776 Positive Predictive Value CentroidAlifold(20): 0.874 PETfold_pre2.0(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.75960267492e-05	+ CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.802 PPfold(20): 0.793 Sensitivity CentroidAlifold(20): 0.734 PPfold(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.880 PPfold(20): 0.841 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 6.38150542963e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.812 IPknot: 0.639 Sensitivity CentroidAlifold(20): 0.745 IPknot: 0.637 Positive Predictive Value CentroidAlifold(20): 0.890 IPknot: 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 MXScarna(20): 0.749 Sensitivity CentroidAlifold(20): 0.728 MXScarna(20): 0.724 Positive Predictive Value CentroidAlifold(20): 0.901 MXScarna(20): 0.780 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNASampler(20): 0.738 Sensitivity CentroidAlifold(20): 0.728 RNASampler(20): 0.667 Positive Predictive Value CentroidAlifold(20): 0.901 RNASampler(20): 0.822 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.802 TurboFold(20): 0.758 Sensitivity CentroidAlifold(20): 0.734 TurboFold(20): 0.748 Positive Predictive Value CentroidAlifold(20): 0.880 TurboFold(20): 0.773 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 CentroidAlifold(seed): 0.695 Sensitivity CentroidAlifold(20): 0.728 CentroidAlifold(seed): 0.528 Positive Predictive Value CentroidAlifold(20): 0.901 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 CentroidFold: 0.690 Sensitivity CentroidAlifold(20): 0.728 CentroidFold: 0.689 Positive Predictive Value CentroidAlifold(20): 0.901 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Sfold: 0.680 Sensitivity CentroidAlifold(20): 0.728 Sfold: 0.667 Positive Predictive Value CentroidAlifold(20): 0.901 Sfold: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.822 CentroidHomfold‑LAST: 0.725 Sensitivity CentroidAlifold(20): 0.763 CentroidHomfold‑LAST: 0.723 Positive Predictive Value CentroidAlifold(20): 0.890 CentroidHomfold‑LAST: 0.733 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Contrafold: 0.649 Sensitivity CentroidAlifold(20): 0.728 Contrafold: 0.675 Positive Predictive Value CentroidAlifold(20): 0.901 Contrafold: 0.631 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.714 RNAalifold(seed): 0.663 Sensitivity CentroidAlifold(20): 0.588 RNAalifold(seed): 0.475 Positive Predictive Value CentroidAlifold(20): 0.871 RNAalifold(seed): 0.932 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.808 MaxExpect: 0.667 Sensitivity CentroidAlifold(20): 0.728 MaxExpect: 0.681 Positive Predictive Value CentroidAlifold(20): 0.901 MaxExpect: 0.661 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.808 HotKnots: 0.645 Sensitivity CentroidAlifold(20): 0.728 HotKnots: 0.677 Positive Predictive Value CentroidAlifold(20): 0.901 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 UNAFold: 0.658 Sensitivity CentroidAlifold(20): 0.728 UNAFold: 0.678 Positive Predictive Value CentroidAlifold(20): 0.901 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.793 ProbKnot: 0.653 Sensitivity CentroidAlifold(20): 0.704 ProbKnot: 0.681 Positive Predictive Value CentroidAlifold(20): 0.898 ProbKnot: 0.632 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Murlet(20): 0.702 Sensitivity CentroidAlifold(20): 0.728 Murlet(20): 0.610 Positive Predictive Value CentroidAlifold(20): 0.901 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.808 PknotsRG: 0.670 Sensitivity CentroidAlifold(20): 0.728 PknotsRG: 0.700 Positive Predictive Value CentroidAlifold(20): 0.901 PknotsRG: 0.648 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAfold: 0.654 Sensitivity CentroidAlifold(20): 0.728 RNAfold: 0.680 Positive Predictive Value CentroidAlifold(20): 0.901 RNAfold: 0.636 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAshapes: 0.651 Sensitivity CentroidAlifold(20): 0.728 RNAshapes: 0.672 Positive Predictive Value CentroidAlifold(20): 0.901 RNAshapes: 0.638 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.793 Fold: 0.664 Sensitivity CentroidAlifold(20): 0.704 Fold: 0.696 Positive Predictive Value CentroidAlifold(20): 0.898 Fold: 0.640 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.690 TurboFold(seed): 0.625 Sensitivity CentroidAlifold(20): 0.576 TurboFold(seed): 0.624 Positive Predictive Value CentroidAlifold(20): 0.832 TurboFold(seed): 0.634 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.759 Afold: 0.613 Sensitivity CentroidAlifold(20): 0.654 Afold: 0.640 Positive Predictive Value CentroidAlifold(20): 0.885 Afold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Carnac(20): 0.695 Sensitivity CentroidAlifold(20): 0.728 Carnac(20): 0.529 Positive Predictive Value CentroidAlifold(20): 0.901 Carnac(20): 0.918 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 RSpredict(20): 0.657 Sensitivity CentroidAlifold(20): 0.726 RSpredict(20): 0.595 Positive Predictive Value CentroidAlifold(20): 0.901 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAsubopt: 0.660 Sensitivity CentroidAlifold(20): 0.728 RNAsubopt: 0.694 Positive Predictive Value CentroidAlifold(20): 0.901 RNAsubopt: 0.634 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.847 Cylofold: 0.711 Sensitivity CentroidAlifold(20): 0.762 Cylofold: 0.714 Positive Predictive Value CentroidAlifold(20): 0.945 Cylofold: 0.717 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 McQFold: 0.607 Sensitivity CentroidAlifold(20): 0.728 McQFold: 0.622 Positive Predictive Value CentroidAlifold(20): 0.901 McQFold: 0.599 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.798 RNASLOpt: 0.559 Sensitivity CentroidAlifold(20): 0.732 RNASLOpt: 0.561 Positive Predictive Value CentroidAlifold(20): 0.874 RNASLOpt: 0.566 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.821 Pknots: 0.585 Sensitivity CentroidAlifold(20): 0.750 Pknots: 0.631 Positive Predictive Value CentroidAlifold(20): 0.903 Pknots: 0.553 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.819 CRWrnafold: 0.668 Sensitivity CentroidAlifold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value CentroidAlifold(20): 0.930 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.799 Multilign(20): 0.625 Sensitivity CentroidAlifold(20): 0.721 Multilign(20): 0.611 Positive Predictive Value CentroidAlifold(20): 0.890 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.621 RNASampler(seed): 0.593 Sensitivity CentroidAlifold(20): 0.517 RNASampler(seed): 0.545 Positive Predictive Value CentroidAlifold(20): 0.752 RNASampler(seed): 0.650 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.886 Alterna: 0.658 Sensitivity CentroidAlifold(20): 0.823 Alterna: 0.667 Positive Predictive Value CentroidAlifold(20): 0.958 Alterna: 0.661 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Mastr(20): 0.610 Sensitivity CentroidAlifold(20): 0.728 Mastr(20): 0.475 Positive Predictive Value CentroidAlifold(20): 0.901 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.817 Vsfold4: 0.526 Sensitivity CentroidAlifold(20): 0.740 Vsfold4: 0.525 Positive Predictive Value CentroidAlifold(20): 0.906 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.722 Murlet(seed): 0.554 Sensitivity CentroidAlifold(20): 0.602 Murlet(seed): 0.350 Positive Predictive Value CentroidAlifold(20): 0.870 Murlet(seed): 0.884 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.815 MCFold: 0.494 Sensitivity CentroidAlifold(20): 0.744 MCFold: 0.554 Positive Predictive Value CentroidAlifold(20): 0.896 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.817 Vsfold5: 0.480 Sensitivity CentroidAlifold(20): 0.740 Vsfold5: 0.486 Positive Predictive Value CentroidAlifold(20): 0.906 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.812 RNAwolf: 0.438 Sensitivity CentroidAlifold(20): 0.745 RNAwolf: 0.454 Positive Predictive Value CentroidAlifold(20): 0.890 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 CMfinder(20): 0.648 Sensitivity CentroidAlifold(20): 0.783 CMfinder(20): 0.563 Positive Predictive Value CentroidAlifold(20): 0.866 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.813 NanoFolder: 0.322 Sensitivity CentroidAlifold(20): 0.761 NanoFolder: 0.414 Positive Predictive Value CentroidAlifold(20): 0.872 NanoFolder: 0.264 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.878 RDfolder: 0.633 Sensitivity CentroidAlifold(20): 0.810 RDfolder: 0.601 Positive Predictive Value CentroidAlifold(20): 0.956 RDfolder: 0.681 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 RSpredict(seed): 0.219 Sensitivity CentroidAlifold(20): 0.726 RSpredict(seed): 0.107 Positive Predictive Value CentroidAlifold(20): 0.901 RSpredict(seed): 0.461 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Multilign(seed): 0.669 Sensitivity CentroidAlifold(20): 0.569 Multilign(seed): 0.632 Positive Predictive Value CentroidAlifold(20): 0.845 Multilign(seed): 0.717 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.809 PPfold(seed): 0.053 Sensitivity CentroidAlifold(20): 0.741 PPfold(seed): 0.010 Positive Predictive Value CentroidAlifold(20): 0.888 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Carnac(seed): 0.173 Sensitivity CentroidAlifold(20): 0.661 Carnac(seed): 0.030 Positive Predictive Value CentroidAlifold(20): 0.884 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.728 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.901 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CentroidAlifold(20): 0.863 Sensitivity PETfold_2.0(seed): 0.889 CentroidAlifold(20): 0.815 Positive Predictive Value PETfold_2.0(seed): 0.923 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidAlifold(20): 0.863 Sensitivity PETfold_2.0(20): 0.889 CentroidAlifold(20): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(seed)	18 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 CentroidAlifold(20): 0.798 Sensitivity PETfold_pre2.0(seed): 0.858 CentroidAlifold(20): 0.732 Positive Predictive Value PETfold_pre2.0(seed): 0.919 CentroidAlifold(20): 0.874 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08		+ PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 ContextFold: 0.805 Sensitivity PETfold_pre2.0(seed): 0.841 ContextFold: 0.784 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ContextFold: 0.827 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.865 MXScarna(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.839 MXScarna(seed): 0.735 Positive Predictive Value PETfold_pre2.0(seed): 0.893 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 RNAalifold(20): 0.761 Sensitivity PETfold_pre2.0(seed): 0.858 RNAalifold(20): 0.714 Positive Predictive Value PETfold_pre2.0(seed): 0.919 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.858 PETfold_pre2.0(20): 0.796 Sensitivity PETfold_pre2.0(seed): 0.820 PETfold_pre2.0(20): 0.768 Positive Predictive Value PETfold_pre2.0(seed): 0.898 PETfold_pre2.0(20): 0.827 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.886 PPfold(20): 0.783 Sensitivity PETfold_pre2.0(seed): 0.856 PPfold(20): 0.749 Positive Predictive Value PETfold_pre2.0(seed): 0.919 PPfold(20): 0.823 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 IPknot: 0.710 Sensitivity PETfold_pre2.0(seed): 0.841 IPknot: 0.700 Positive Predictive Value PETfold_pre2.0(seed): 0.892 IPknot: 0.722 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 MXScarna(20): 0.697 Sensitivity PETfold_pre2.0(seed): 0.858 MXScarna(20): 0.680 Positive Predictive Value PETfold_pre2.0(seed): 0.919 MXScarna(20): 0.721 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 RNASampler(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.858 RNASampler(20): 0.643 Positive Predictive Value PETfold_pre2.0(seed): 0.919 RNASampler(20): 0.745 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.886 TurboFold(20): 0.742 Sensitivity PETfold_pre2.0(seed): 0.856 TurboFold(20): 0.737 Positive Predictive Value PETfold_pre2.0(seed): 0.919 TurboFold(20): 0.753 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 CentroidAlifold(seed): 0.762 Sensitivity PETfold_pre2.0(seed): 0.841 CentroidAlifold(seed): 0.625 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 CentroidFold: 0.698 Sensitivity PETfold_pre2.0(seed): 0.841 CentroidFold: 0.689 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Sfold: 0.612 Sensitivity PETfold_pre2.0(seed): 0.841 Sfold: 0.608 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Sfold: 0.619 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.876 CentroidHomfold‑LAST: 0.691 Sensitivity PETfold_pre2.0(seed): 0.839 CentroidHomfold‑LAST: 0.693 Positive Predictive Value PETfold_pre2.0(seed): 0.916 CentroidHomfold‑LAST: 0.696 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Contrafold: 0.689 Sensitivity PETfold_pre2.0(seed): 0.841 Contrafold: 0.703 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Contrafold: 0.677 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.826 RNAalifold(seed): 0.767 Sensitivity PETfold_pre2.0(seed): 0.794 RNAalifold(seed): 0.670 Positive Predictive Value PETfold_pre2.0(seed): 0.860 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 MaxExpect: 0.617 Sensitivity PETfold_pre2.0(seed): 0.841 MaxExpect: 0.627 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MaxExpect: 0.609 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 HotKnots: 0.610 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.646 Positive Predictive Value PETfold_pre2.0(seed): 0.913 HotKnots: 0.584 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 UNAFold: 0.572 Sensitivity PETfold_pre2.0(seed): 0.841 UNAFold: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.892 UNAFold: 0.557 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 ProbKnot: 0.622 Sensitivity PETfold_pre2.0(seed): 0.841 ProbKnot: 0.637 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Murlet(20): 0.682 Sensitivity PETfold_pre2.0(seed): 0.858 Murlet(20): 0.611 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 PknotsRG: 0.668 Sensitivity PETfold_pre2.0(seed): 0.826 PknotsRG: 0.701 Positive Predictive Value PETfold_pre2.0(seed): 0.913 PknotsRG: 0.644 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 RNAfold: 0.606 Sensitivity PETfold_pre2.0(seed): 0.841 RNAfold: 0.625 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAfold: 0.589 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNAshapes: 0.596 Sensitivity PETfold_pre2.0(seed): 0.826 RNAshapes: 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNAshapes: 0.583 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Fold: 0.590 Sensitivity PETfold_pre2.0(seed): 0.841 Fold: 0.616 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Fold: 0.567 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.789 TurboFold(seed): 0.608 Sensitivity PETfold_pre2.0(seed): 0.721 TurboFold(seed): 0.600 Positive Predictive Value PETfold_pre2.0(seed): 0.867 TurboFold(seed): 0.625 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Afold: 0.538 Sensitivity PETfold_pre2.0(seed): 0.706 Afold: 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.842 Afold: 0.520 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Carnac(20): 0.665 Sensitivity PETfold_pre2.0(seed): 0.858 Carnac(20): 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.856 RSpredict(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.817 RSpredict(20): 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.897 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNAsubopt: 0.635 Sensitivity PETfold_pre2.0(seed): 0.826 RNAsubopt: 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNAsubopt: 0.611 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.854 Cylofold: 0.655 Sensitivity PETfold_pre2.0(seed): 0.811 Cylofold: 0.637 Positive Predictive Value PETfold_pre2.0(seed): 0.905 Cylofold: 0.685 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 McQFold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.841 McQFold: 0.588 Positive Predictive Value PETfold_pre2.0(seed): 0.892 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNASLOpt: 0.591 Sensitivity PETfold_pre2.0(seed): 0.826 RNASLOpt: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 Pknots: 0.550 Sensitivity PETfold_pre2.0(seed): 0.826 Pknots: 0.587 Positive Predictive Value PETfold_pre2.0(seed): 0.913 Pknots: 0.525 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.94031556815e-08	? PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.816 CRWrnafold: 0.636 Sensitivity PETfold_pre2.0(seed): 0.761 CRWrnafold: 0.639 Positive Predictive Value PETfold_pre2.0(seed): 0.881 CRWrnafold: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.898 Multilign(20): 0.620 Sensitivity PETfold_pre2.0(seed): 0.877 Multilign(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.923 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.29018360962e-08	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNASampler(seed): 0.390 Sensitivity PETfold_pre2.0(seed): 0.652 RNASampler(seed): 0.323 Positive Predictive Value PETfold_pre2.0(seed): 0.837 RNASampler(seed): 0.481 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.812 Alterna: 0.648 Sensitivity PETfold_pre2.0(seed): 0.745 Alterna: 0.655 Positive Predictive Value PETfold_pre2.0(seed): 0.891 Alterna: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Mastr(20): 0.577 Sensitivity PETfold_pre2.0(seed): 0.858 Mastr(20): 0.471 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Mastr(20): 0.715 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.878 Vsfold4: 0.538 Sensitivity PETfold_pre2.0(seed): 0.842 Vsfold4: 0.533 Positive Predictive Value PETfold_pre2.0(seed): 0.918 Vsfold4: 0.554 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Murlet(seed): 0.473 Sensitivity PETfold_pre2.0(seed): 0.697 Murlet(seed): 0.300 Positive Predictive Value PETfold_pre2.0(seed): 0.853 Murlet(seed): 0.756 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.863 MCFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.823 MCFold: 0.524 Positive Predictive Value PETfold_pre2.0(seed): 0.907 MCFold: 0.439 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.876 Vsfold5: 0.481 Sensitivity PETfold_pre2.0(seed): 0.839 Vsfold5: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.916 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 RNAwolf: 0.494 Sensitivity PETfold_pre2.0(seed): 0.841 RNAwolf: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAwolf: 0.495 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.917 CMfinder(20): 0.648 Sensitivity PETfold_pre2.0(seed): 0.908 CMfinder(20): 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.929 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.883 NanoFolder: 0.340 Sensitivity PETfold_pre2.0(seed): 0.848 NanoFolder: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.922 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.801 RDfolder: 0.432 Sensitivity PETfold_pre2.0(seed): 0.749 RDfolder: 0.398 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.493 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.853 RSpredict(seed): 0.515 Sensitivity PETfold_pre2.0(seed): 0.822 RSpredict(seed): 0.388 Positive Predictive Value PETfold_pre2.0(seed): 0.885 RSpredict(seed): 0.686 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.766 Multilign(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.686 Multilign(seed): 0.575 Positive Predictive Value PETfold_pre2.0(seed): 0.861 Multilign(seed): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.865 PPfold(seed): 0.166 Sensitivity PETfold_pre2.0(seed): 0.823 PPfold(seed): 0.045 Positive Predictive Value PETfold_pre2.0(seed): 0.912 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Carnac(seed): 0.562 Sensitivity PETfold_pre2.0(seed): 0.804 Carnac(seed): 0.339 Positive Predictive Value PETfold_pre2.0(seed): 0.867 Carnac(seed): 0.934 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 Mastr(seed): 0.042 Sensitivity PETfold_pre2.0(seed): 0.826 Mastr(seed): 0.005 Positive Predictive Value PETfold_pre2.0(seed): 0.913 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.874 PETfold_2.0(seed): 0.866 Sensitivity PETfold_pre2.0(seed): 0.845 PETfold_2.0(seed): 0.845 Positive Predictive Value PETfold_pre2.0(seed): 0.907 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.905 PETfold_2.0(20): 0.905 Sensitivity PETfold_pre2.0(seed): 0.889 PETfold_2.0(20): 0.889 Positive Predictive Value PETfold_pre2.0(seed): 0.923 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
ContextFold	18 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.798 ContextFold: 0.748 Sensitivity CentroidAlifold(20): 0.732 ContextFold: 0.730 Positive Predictive Value CentroidAlifold(20): 0.874 ContextFold: 0.772 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	26 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 ContextFold: 0.805 Sensitivity PETfold_pre2.0(seed): 0.841 ContextFold: 0.784 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ContextFold: 0.827 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.830 MXScarna(seed): 0.775 Sensitivity ContextFold: 0.800 MXScarna(seed): 0.740 Positive Predictive Value ContextFold: 0.861 MXScarna(seed): 0.813 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.781 RNAalifold(20): 0.759 Sensitivity ContextFold: 0.731 RNAalifold(20): 0.688 Positive Predictive Value ContextFold: 0.840 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08	- PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 ContextFold: 0.748 Sensitivity PETfold_pre2.0(20): 0.776 ContextFold: 0.730 Positive Predictive Value PETfold_pre2.0(20): 0.815 ContextFold: 0.772 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	- PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.802 ContextFold: 0.781 Sensitivity PPfold(20): 0.749 ContextFold: 0.731 Positive Predictive Value PPfold(20): 0.864 ContextFold: 0.840 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.65163701526e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.680 IPknot: 0.663 Sensitivity ContextFold: 0.671 IPknot: 0.633 Positive Predictive Value ContextFold: 0.689 IPknot: 0.695 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 5.84585956207e-05	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.781 MXScarna(20): 0.670 Sensitivity ContextFold: 0.731 MXScarna(20): 0.627 Positive Predictive Value ContextFold: 0.840 MXScarna(20): 0.723 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.07229227445e-09	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.781 RNASampler(20): 0.690 Sensitivity ContextFold: 0.731 RNASampler(20): 0.616 Positive Predictive Value ContextFold: 0.840 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.781 TurboFold(20): 0.755 Sensitivity ContextFold: 0.731 TurboFold(20): 0.717 Positive Predictive Value ContextFold: 0.840 TurboFold(20): 0.800 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.805 CentroidAlifold(seed): 0.762 Sensitivity ContextFold: 0.784 CentroidAlifold(seed): 0.625 Positive Predictive Value ContextFold: 0.827 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.683 CentroidFold: 0.614 Sensitivity ContextFold: 0.677 CentroidFold: 0.600 Positive Predictive Value ContextFold: 0.691 CentroidFold: 0.631 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.680 Sfold: 0.592 Sensitivity ContextFold: 0.671 Sfold: 0.596 Positive Predictive Value ContextFold: 0.689 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.787 CentroidHomfold‑LAST: 0.677 Sensitivity ContextFold: 0.765 CentroidHomfold‑LAST: 0.601 Positive Predictive Value ContextFold: 0.812 CentroidHomfold‑LAST: 0.767 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.680 Contrafold: 0.592 Sensitivity ContextFold: 0.671 Contrafold: 0.607 Positive Predictive Value ContextFold: 0.689 Contrafold: 0.580 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.796 RNAalifold(seed): 0.785 Sensitivity ContextFold: 0.770 RNAalifold(seed): 0.708 Positive Predictive Value ContextFold: 0.823 RNAalifold(seed): 0.872 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.39974817869e-07	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.680 MaxExpect: 0.572 Sensitivity ContextFold: 0.671 MaxExpect: 0.588 Positive Predictive Value ContextFold: 0.689 MaxExpect: 0.557 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.760 HotKnots: 0.661 Sensitivity ContextFold: 0.742 HotKnots: 0.689 Positive Predictive Value ContextFold: 0.784 HotKnots: 0.640 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.680 UNAFold: 0.562 Sensitivity ContextFold: 0.671 UNAFold: 0.588 Positive Predictive Value ContextFold: 0.689 UNAFold: 0.540 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.680 ProbKnot: 0.569 Sensitivity ContextFold: 0.671 ProbKnot: 0.594 Positive Predictive Value ContextFold: 0.689 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.781 Murlet(20): 0.625 Sensitivity ContextFold: 0.731 Murlet(20): 0.548 Positive Predictive Value ContextFold: 0.840 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.612 PknotsRG: 0.573 Sensitivity ContextFold: 0.604 PknotsRG: 0.608 Positive Predictive Value ContextFold: 0.622 PknotsRG: 0.541 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.680 RNAfold: 0.566 Sensitivity ContextFold: 0.671 RNAfold: 0.592 Positive Predictive Value ContextFold: 0.689 RNAfold: 0.542 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.760 RNAshapes: 0.618 Sensitivity ContextFold: 0.742 RNAshapes: 0.638 Positive Predictive Value ContextFold: 0.784 RNAshapes: 0.605 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.680 Fold: 0.528 Sensitivity ContextFold: 0.671 Fold: 0.561 Positive Predictive Value ContextFold: 0.689 Fold: 0.499 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.606 TurboFold(seed): 0.576 Sensitivity ContextFold: 0.560 TurboFold(seed): 0.545 Positive Predictive Value ContextFold: 0.665 TurboFold(seed): 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	= ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.513 Afold: 0.508 Sensitivity ContextFold: 0.515 Afold: 0.546 Positive Predictive Value ContextFold: 0.512 Afold: 0.474 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.001244508652	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.781 Carnac(20): 0.612 Sensitivity ContextFold: 0.731 Carnac(20): 0.466 Positive Predictive Value ContextFold: 0.840 Carnac(20): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.19192530585e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.733 RSpredict(20): 0.593 Sensitivity ContextFold: 0.715 RSpredict(20): 0.539 Positive Predictive Value ContextFold: 0.757 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.760 RNAsubopt: 0.611 Sensitivity ContextFold: 0.742 RNAsubopt: 0.645 Positive Predictive Value ContextFold: 0.784 RNAsubopt: 0.584 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.783 Cylofold: 0.612 Sensitivity ContextFold: 0.758 Cylofold: 0.598 Positive Predictive Value ContextFold: 0.816 Cylofold: 0.638 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.677 McQFold: 0.469 Sensitivity ContextFold: 0.668 McQFold: 0.482 Positive Predictive Value ContextFold: 0.686 McQFold: 0.457 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.760 RNASLOpt: 0.580 Sensitivity ContextFold: 0.742 RNASLOpt: 0.559 Positive Predictive Value ContextFold: 0.784 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.755 Pknots: 0.577 Sensitivity ContextFold: 0.726 Pknots: 0.606 Positive Predictive Value ContextFold: 0.792 Pknots: 0.560 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.799 CRWrnafold: 0.688 Sensitivity ContextFold: 0.762 CRWrnafold: 0.684 Positive Predictive Value ContextFold: 0.844 CRWrnafold: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.820 Multilign(20): 0.657 Sensitivity ContextFold: 0.768 Multilign(20): 0.644 Positive Predictive Value ContextFold: 0.881 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.20383511129e-08	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.577 RNASampler(seed): 0.371 Sensitivity ContextFold: 0.550 RNASampler(seed): 0.290 Positive Predictive Value ContextFold: 0.611 RNASampler(seed): 0.483 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.782 Alterna: 0.691 Sensitivity ContextFold: 0.757 Alterna: 0.701 Positive Predictive Value ContextFold: 0.820 Alterna: 0.697 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.07842257011e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.781 Mastr(20): 0.561 Sensitivity ContextFold: 0.731 Mastr(20): 0.430 Positive Predictive Value ContextFold: 0.840 Mastr(20): 0.741 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.773 Vsfold4: 0.583 Sensitivity ContextFold: 0.750 Vsfold4: 0.572 Positive Predictive Value ContextFold: 0.803 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.605 Murlet(seed): 0.470 Sensitivity ContextFold: 0.559 Murlet(seed): 0.313 Positive Predictive Value ContextFold: 0.663 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.718 MCFold: 0.541 Sensitivity ContextFold: 0.700 MCFold: 0.576 Positive Predictive Value ContextFold: 0.743 MCFold: 0.519 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.784 Vsfold5: 0.507 Sensitivity ContextFold: 0.759 Vsfold5: 0.514 Positive Predictive Value ContextFold: 0.816 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.683 RNAwolf: 0.418 Sensitivity ContextFold: 0.677 RNAwolf: 0.428 Positive Predictive Value ContextFold: 0.691 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.908 CMfinder(20): 0.652 Sensitivity ContextFold: 0.860 CMfinder(20): 0.518 Positive Predictive Value ContextFold: 0.961 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.738 NanoFolder: 0.394 Sensitivity ContextFold: 0.717 NanoFolder: 0.485 Positive Predictive Value ContextFold: 0.765 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.776 RDfolder: 0.546 Sensitivity ContextFold: 0.734 RDfolder: 0.494 Positive Predictive Value ContextFold: 0.832 RDfolder: 0.625 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.800 RSpredict(seed): 0.480 Sensitivity ContextFold: 0.779 RSpredict(seed): 0.353 Positive Predictive Value ContextFold: 0.823 RSpredict(seed): 0.655 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.601 Multilign(seed): 0.554 Sensitivity ContextFold: 0.569 Multilign(seed): 0.489 Positive Predictive Value ContextFold: 0.645 Multilign(seed): 0.638 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.767 PPfold(seed): 0.102 Sensitivity ContextFold: 0.719 PPfold(seed): 0.023 Positive Predictive Value ContextFold: 0.823 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.805 Carnac(seed): 0.575 Sensitivity ContextFold: 0.779 Carnac(seed): 0.356 Positive Predictive Value ContextFold: 0.833 Carnac(seed): 0.929 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.767 Mastr(seed): 0.000 Sensitivity ContextFold: 0.719 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.823 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	? ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.938 PETfold_2.0(seed): 0.866 Sensitivity ContextFold: 0.914 PETfold_2.0(seed): 0.845 Positive Predictive Value ContextFold: 0.964 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.981 PETfold_2.0(20): 0.905 Sensitivity ContextFold: 0.963 PETfold_2.0(20): 0.889 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MXScarna(seed)	38 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 MXScarna(seed): 0.769 Sensitivity CentroidAlifold(20): 0.724 MXScarna(seed): 0.731 Positive Predictive Value CentroidAlifold(20): 0.903 MXScarna(seed): 0.814 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.865 MXScarna(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.839 MXScarna(seed): 0.735 Positive Predictive Value PETfold_pre2.0(seed): 0.893 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.830 MXScarna(seed): 0.775 Sensitivity ContextFold: 0.800 MXScarna(seed): 0.740 Positive Predictive Value ContextFold: 0.861 MXScarna(seed): 0.813 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.43692248862e-08		- RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.785 MXScarna(seed): 0.775 Sensitivity RNAalifold(20): 0.698 MXScarna(seed): 0.732 Positive Predictive Value RNAalifold(20): 0.887 MXScarna(seed): 0.825 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.90954827572e-07	- PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.789 MXScarna(seed): 0.730 Sensitivity PETfold_pre2.0(20): 0.770 MXScarna(seed): 0.691 Positive Predictive Value PETfold_pre2.0(20): 0.813 MXScarna(seed): 0.777 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	- PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.812 MXScarna(seed): 0.736 Sensitivity PPfold(20): 0.753 MXScarna(seed): 0.688 Positive Predictive Value PPfold(20): 0.880 MXScarna(seed): 0.794 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.781 IPknot: 0.745 Sensitivity MXScarna(seed): 0.745 IPknot: 0.717 Positive Predictive Value MXScarna(seed): 0.819 IPknot: 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.00017354801e-07	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 MXScarna(20): 0.754 Sensitivity MXScarna(seed): 0.732 MXScarna(20): 0.718 Positive Predictive Value MXScarna(seed): 0.825 MXScarna(20): 0.796 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 RNASampler(20): 0.752 Sensitivity MXScarna(seed): 0.732 RNASampler(20): 0.667 Positive Predictive Value MXScarna(seed): 0.825 RNASampler(20): 0.853 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.00387151331e-07	- TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.773 MXScarna(seed): 0.736 Sensitivity TurboFold(20): 0.737 MXScarna(seed): 0.688 Positive Predictive Value TurboFold(20): 0.817 MXScarna(seed): 0.794 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.780 CentroidAlifold(seed): 0.735 Sensitivity MXScarna(seed): 0.744 CentroidAlifold(seed): 0.605 Positive Predictive Value MXScarna(seed): 0.819 CentroidAlifold(seed): 0.894 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.780 CentroidFold: 0.718 Sensitivity MXScarna(seed): 0.744 CentroidFold: 0.718 Positive Predictive Value MXScarna(seed): 0.819 CentroidFold: 0.721 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.786 Sfold: 0.671 Sensitivity MXScarna(seed): 0.749 Sfold: 0.665 Positive Predictive Value MXScarna(seed): 0.825 Sfold: 0.680 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.743 CentroidHomfold‑LAST: 0.728 Sensitivity MXScarna(seed): 0.700 CentroidHomfold‑LAST: 0.715 Positive Predictive Value MXScarna(seed): 0.798 CentroidHomfold‑LAST: 0.749 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.66134940242e-07	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.786 Contrafold: 0.707 Sensitivity MXScarna(seed): 0.749 Contrafold: 0.727 Positive Predictive Value MXScarna(seed): 0.825 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.749 RNAalifold(seed): 0.740 Sensitivity MXScarna(seed): 0.710 RNAalifold(seed): 0.624 Positive Predictive Value MXScarna(seed): 0.792 RNAalifold(seed): 0.879 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.03703286746e-07	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.781 MaxExpect: 0.676 Sensitivity MXScarna(seed): 0.746 MaxExpect: 0.690 Positive Predictive Value MXScarna(seed): 0.819 MaxExpect: 0.664 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.769 HotKnots: 0.676 Sensitivity MXScarna(seed): 0.727 HotKnots: 0.706 Positive Predictive Value MXScarna(seed): 0.819 HotKnots: 0.653 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.786 UNAFold: 0.655 Sensitivity MXScarna(seed): 0.749 UNAFold: 0.673 Positive Predictive Value MXScarna(seed): 0.825 UNAFold: 0.640 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.769 ProbKnot: 0.648 Sensitivity MXScarna(seed): 0.733 ProbKnot: 0.671 Positive Predictive Value MXScarna(seed): 0.807 ProbKnot: 0.627 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Murlet(20): 0.688 Sensitivity MXScarna(seed): 0.732 Murlet(20): 0.589 Positive Predictive Value MXScarna(seed): 0.825 Murlet(20): 0.810 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.769 PknotsRG: 0.691 Sensitivity MXScarna(seed): 0.727 PknotsRG: 0.717 Positive Predictive Value MXScarna(seed): 0.819 PknotsRG: 0.671 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.786 RNAfold: 0.661 Sensitivity MXScarna(seed): 0.749 RNAfold: 0.682 Positive Predictive Value MXScarna(seed): 0.825 RNAfold: 0.642 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.769 RNAshapes: 0.685 Sensitivity MXScarna(seed): 0.727 RNAshapes: 0.704 Positive Predictive Value MXScarna(seed): 0.819 RNAshapes: 0.673 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.774 Fold: 0.663 Sensitivity MXScarna(seed): 0.739 Fold: 0.689 Positive Predictive Value MXScarna(seed): 0.812 Fold: 0.640 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 MXScarna(seed): 0.633 Sensitivity TurboFold(seed): 0.615 MXScarna(seed): 0.580 Positive Predictive Value TurboFold(seed): 0.691 MXScarna(seed): 0.700 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.69659660552e-05	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.762 Afold: 0.659 Sensitivity MXScarna(seed): 0.714 Afold: 0.691 Positive Predictive Value MXScarna(seed): 0.818 Afold: 0.634 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Carnac(20): 0.685 Sensitivity MXScarna(seed): 0.732 Carnac(20): 0.517 Positive Predictive Value MXScarna(seed): 0.825 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.769 RSpredict(20): 0.656 Sensitivity MXScarna(seed): 0.731 RSpredict(20): 0.593 Positive Predictive Value MXScarna(seed): 0.814 RSpredict(20): 0.733 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.769 RNAsubopt: 0.667 Sensitivity MXScarna(seed): 0.727 RNAsubopt: 0.694 Positive Predictive Value MXScarna(seed): 0.819 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.775 Cylofold: 0.706 Sensitivity MXScarna(seed): 0.734 Cylofold: 0.693 Positive Predictive Value MXScarna(seed): 0.826 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.786 McQFold: 0.637 Sensitivity MXScarna(seed): 0.749 McQFold: 0.643 Positive Predictive Value MXScarna(seed): 0.825 McQFold: 0.634 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.711 RNASLOpt: 0.617 Sensitivity MXScarna(seed): 0.658 RNASLOpt: 0.587 Positive Predictive Value MXScarna(seed): 0.776 RNASLOpt: 0.657 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.789 Pknots: 0.692 Sensitivity MXScarna(seed): 0.746 Pknots: 0.722 Positive Predictive Value MXScarna(seed): 0.841 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.705 CRWrnafold: 0.647 Sensitivity MXScarna(seed): 0.660 CRWrnafold: 0.655 Positive Predictive Value MXScarna(seed): 0.761 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.759 Multilign(20): 0.652 Sensitivity MXScarna(seed): 0.717 Multilign(20): 0.624 Positive Predictive Value MXScarna(seed): 0.810 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.734 RNASampler(seed): 0.728 Sensitivity MXScarna(seed): 0.688 RNASampler(seed): 0.634 Positive Predictive Value MXScarna(seed): 0.791 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.79687093416e-07	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.828 Alterna: 0.757 Sensitivity MXScarna(seed): 0.776 Alterna: 0.765 Positive Predictive Value MXScarna(seed): 0.892 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Mastr(20): 0.618 Sensitivity MXScarna(seed): 0.732 Mastr(20): 0.469 Positive Predictive Value MXScarna(seed): 0.825 Mastr(20): 0.821 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.779 Vsfold4: 0.613 Sensitivity MXScarna(seed): 0.738 Vsfold4: 0.610 Positive Predictive Value MXScarna(seed): 0.826 Vsfold4: 0.623 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.735 Murlet(seed): 0.594 Sensitivity MXScarna(seed): 0.689 Murlet(seed): 0.418 Positive Predictive Value MXScarna(seed): 0.792 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.776 MCFold: 0.557 Sensitivity MXScarna(seed): 0.736 MCFold: 0.608 Positive Predictive Value MXScarna(seed): 0.824 MCFold: 0.522 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.777 Vsfold5: 0.567 Sensitivity MXScarna(seed): 0.737 Vsfold5: 0.569 Positive Predictive Value MXScarna(seed): 0.824 Vsfold5: 0.574 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.774 RNAwolf: 0.502 Sensitivity MXScarna(seed): 0.740 RNAwolf: 0.502 Positive Predictive Value MXScarna(seed): 0.810 RNAwolf: 0.503 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.776 CMfinder(20): 0.652 Sensitivity MXScarna(seed): 0.737 CMfinder(20): 0.518 Positive Predictive Value MXScarna(seed): 0.824 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.753 NanoFolder: 0.338 Sensitivity MXScarna(seed): 0.712 NanoFolder: 0.414 Positive Predictive Value MXScarna(seed): 0.802 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.808 RDfolder: 0.626 Sensitivity MXScarna(seed): 0.754 RDfolder: 0.592 Positive Predictive Value MXScarna(seed): 0.874 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.780 RSpredict(seed): 0.453 Sensitivity MXScarna(seed): 0.745 RSpredict(seed): 0.307 Positive Predictive Value MXScarna(seed): 0.819 RSpredict(seed): 0.670 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 MXScarna(seed): 0.629 Sensitivity Multilign(seed): 0.591 MXScarna(seed): 0.582 Positive Predictive Value Multilign(seed): 0.724 MXScarna(seed): 0.691 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.732 PPfold(seed): 0.094 Sensitivity MXScarna(seed): 0.681 PPfold(seed): 0.019 Positive Predictive Value MXScarna(seed): 0.793 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.784 Carnac(seed): 0.474 Sensitivity MXScarna(seed): 0.750 Carnac(seed): 0.239 Positive Predictive Value MXScarna(seed): 0.820 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.769 Mastr(seed): 0.282 Sensitivity MXScarna(seed): 0.727 Mastr(seed): 0.089 Positive Predictive Value MXScarna(seed): 0.819 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient MXScarna(seed): 0.884 PETfold_2.0(seed): 0.866 Sensitivity MXScarna(seed): 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value MXScarna(seed): 0.909 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 MXScarna(seed): 0.845 Sensitivity PETfold_2.0(20): 0.889 MXScarna(seed): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 MXScarna(seed): 0.880 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAalifold(20)	39 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAalifold(20): 0.783 Sensitivity CentroidAlifold(20): 0.728 RNAalifold(20): 0.710 Positive Predictive Value CentroidAlifold(20): 0.901 RNAalifold(20): 0.867 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 RNAalifold(20): 0.761 Sensitivity PETfold_pre2.0(seed): 0.858 RNAalifold(20): 0.714 Positive Predictive Value PETfold_pre2.0(seed): 0.919 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.24270395587e-08	11 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.781 RNAalifold(20): 0.759 Sensitivity ContextFold: 0.731 RNAalifold(20): 0.688 Positive Predictive Value ContextFold: 0.840 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08	33 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.785 MXScarna(seed): 0.775 Sensitivity RNAalifold(20): 0.698 MXScarna(seed): 0.732 Positive Predictive Value RNAalifold(20): 0.887 MXScarna(seed): 0.825 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.90954827572e-07		- PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAalifold(20): 0.761 Sensitivity PETfold_pre2.0(20): 0.776 RNAalifold(20): 0.714 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	- PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.812 RNAalifold(20): 0.771 Sensitivity PPfold(20): 0.753 RNAalifold(20): 0.710 Positive Predictive Value PPfold(20): 0.880 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.784 IPknot: 0.712 Sensitivity RNAalifold(20): 0.721 IPknot: 0.678 Positive Predictive Value RNAalifold(20): 0.858 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 MXScarna(20): 0.755 Sensitivity RNAalifold(20): 0.704 MXScarna(20): 0.720 Positive Predictive Value RNAalifold(20): 0.891 MXScarna(20): 0.796 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 RNASampler(20): 0.751 Sensitivity RNAalifold(20): 0.704 RNASampler(20): 0.663 Positive Predictive Value RNAalifold(20): 0.891 RNASampler(20): 0.856 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.773 RNAalifold(20): 0.771 Sensitivity TurboFold(20): 0.737 RNAalifold(20): 0.710 Positive Predictive Value TurboFold(20): 0.817 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.149956528961	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.783 CentroidAlifold(seed): 0.695 Sensitivity RNAalifold(20): 0.710 CentroidAlifold(seed): 0.528 Positive Predictive Value RNAalifold(20): 0.867 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.783 CentroidFold: 0.690 Sensitivity RNAalifold(20): 0.710 CentroidFold: 0.689 Positive Predictive Value RNAalifold(20): 0.867 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.790 Sfold: 0.707 Sensitivity RNAalifold(20): 0.704 Sfold: 0.683 Positive Predictive Value RNAalifold(20): 0.891 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.796 CentroidHomfold‑LAST: 0.760 Sensitivity RNAalifold(20): 0.735 CentroidHomfold‑LAST: 0.744 Positive Predictive Value RNAalifold(20): 0.868 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.85493025655e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.790 Contrafold: 0.664 Sensitivity RNAalifold(20): 0.704 Contrafold: 0.681 Positive Predictive Value RNAalifold(20): 0.891 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.692 RNAalifold(seed): 0.672 Sensitivity RNAalifold(20): 0.583 RNAalifold(seed): 0.488 Positive Predictive Value RNAalifold(20): 0.827 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23907313115e-07	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.787 MaxExpect: 0.690 Sensitivity RNAalifold(20): 0.701 MaxExpect: 0.693 Positive Predictive Value RNAalifold(20): 0.887 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.790 HotKnots: 0.668 Sensitivity RNAalifold(20): 0.704 HotKnots: 0.692 Positive Predictive Value RNAalifold(20): 0.891 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.790 UNAFold: 0.692 Sensitivity RNAalifold(20): 0.704 UNAFold: 0.701 Positive Predictive Value RNAalifold(20): 0.891 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.762 ProbKnot: 0.679 Sensitivity RNAalifold(20): 0.669 ProbKnot: 0.700 Positive Predictive Value RNAalifold(20): 0.872 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Murlet(20): 0.693 Sensitivity RNAalifold(20): 0.704 Murlet(20): 0.594 Positive Predictive Value RNAalifold(20): 0.891 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.790 PknotsRG: 0.687 Sensitivity RNAalifold(20): 0.704 PknotsRG: 0.709 Positive Predictive Value RNAalifold(20): 0.891 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAfold: 0.677 Sensitivity RNAalifold(20): 0.704 RNAfold: 0.694 Positive Predictive Value RNAalifold(20): 0.891 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAshapes: 0.685 Sensitivity RNAalifold(20): 0.704 RNAshapes: 0.694 Positive Predictive Value RNAalifold(20): 0.891 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.762 Fold: 0.694 Sensitivity RNAalifold(20): 0.669 Fold: 0.715 Positive Predictive Value RNAalifold(20): 0.872 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 RNAalifold(20): 0.663 Sensitivity TurboFold(seed): 0.653 RNAalifold(20): 0.602 Positive Predictive Value TurboFold(seed): 0.723 RNAalifold(20): 0.739 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.744 Afold: 0.639 Sensitivity RNAalifold(20): 0.648 Afold: 0.658 Positive Predictive Value RNAalifold(20): 0.858 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Carnac(20): 0.686 Sensitivity RNAalifold(20): 0.704 Carnac(20): 0.518 Positive Predictive Value RNAalifold(20): 0.891 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.779 RSpredict(20): 0.660 Sensitivity RNAalifold(20): 0.704 RSpredict(20): 0.597 Positive Predictive Value RNAalifold(20): 0.866 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAsubopt: 0.660 Sensitivity RNAalifold(20): 0.704 RNAsubopt: 0.684 Positive Predictive Value RNAalifold(20): 0.891 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.820 Cylofold: 0.715 Sensitivity RNAalifold(20): 0.732 Cylofold: 0.713 Positive Predictive Value RNAalifold(20): 0.925 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.82974185391e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.790 McQFold: 0.641 Sensitivity RNAalifold(20): 0.704 McQFold: 0.648 Positive Predictive Value RNAalifold(20): 0.891 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.759 RNASLOpt: 0.635 Sensitivity RNAalifold(20): 0.688 RNASLOpt: 0.616 Positive Predictive Value RNAalifold(20): 0.842 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.806 Pknots: 0.619 Sensitivity RNAalifold(20): 0.730 Pknots: 0.663 Positive Predictive Value RNAalifold(20): 0.893 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.735 CRWrnafold: 0.668 Sensitivity RNAalifold(20): 0.677 CRWrnafold: 0.683 Positive Predictive Value RNAalifold(20): 0.804 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.770 Multilign(20): 0.652 Sensitivity RNAalifold(20): 0.685 Multilign(20): 0.624 Positive Predictive Value RNAalifold(20): 0.871 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 RNAalifold(20): 0.610 Sensitivity RNASampler(seed): 0.604 RNAalifold(20): 0.578 Positive Predictive Value RNASampler(seed): 0.748 RNAalifold(20): 0.651 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.865 Alterna: 0.671 Sensitivity RNAalifold(20): 0.803 Alterna: 0.680 Positive Predictive Value RNAalifold(20): 0.937 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Mastr(20): 0.620 Sensitivity RNAalifold(20): 0.704 Mastr(20): 0.473 Positive Predictive Value RNAalifold(20): 0.891 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.802 Vsfold4: 0.561 Sensitivity RNAalifold(20): 0.714 Vsfold4: 0.556 Positive Predictive Value RNAalifold(20): 0.904 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.701 Murlet(seed): 0.557 Sensitivity RNAalifold(20): 0.603 Murlet(seed): 0.355 Positive Predictive Value RNAalifold(20): 0.821 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.786 MCFold: 0.499 Sensitivity RNAalifold(20): 0.728 MCFold: 0.560 Positive Predictive Value RNAalifold(20): 0.854 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.802 Vsfold5: 0.494 Sensitivity RNAalifold(20): 0.714 Vsfold5: 0.496 Positive Predictive Value RNAalifold(20): 0.904 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.778 RNAwolf: 0.438 Sensitivity RNAalifold(20): 0.733 RNAwolf: 0.454 Positive Predictive Value RNAalifold(20): 0.831 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.888 CMfinder(20): 0.652 Sensitivity RNAalifold(20): 0.816 CMfinder(20): 0.518 Positive Predictive Value RNAalifold(20): 0.969 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.788 NanoFolder: 0.329 Sensitivity RNAalifold(20): 0.732 NanoFolder: 0.405 Positive Predictive Value RNAalifold(20): 0.853 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.847 RDfolder: 0.636 Sensitivity RNAalifold(20): 0.764 RDfolder: 0.602 Positive Predictive Value RNAalifold(20): 0.945 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.779 RSpredict(seed): 0.230 Sensitivity RNAalifold(20): 0.704 RSpredict(seed): 0.114 Positive Predictive Value RNAalifold(20): 0.866 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 RNAalifold(20): 0.708 Sensitivity Multilign(seed): 0.682 RNAalifold(20): 0.651 Positive Predictive Value Multilign(seed): 0.793 RNAalifold(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.784 PPfold(seed): 0.046 Sensitivity RNAalifold(20): 0.721 PPfold(seed): 0.009 Positive Predictive Value RNAalifold(20): 0.858 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.744 Carnac(seed): 0.220 Sensitivity RNAalifold(20): 0.657 Carnac(seed): 0.049 Positive Predictive Value RNAalifold(20): 0.849 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.790 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 RNAalifold(20): 0.863 Sensitivity PETfold_2.0(seed): 0.889 RNAalifold(20): 0.815 Positive Predictive Value PETfold_2.0(seed): 0.923 RNAalifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAalifold(20): 0.863 Sensitivity PETfold_2.0(20): 0.889 RNAalifold(20): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 RNAalifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(20)	18 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.798 PETfold_pre2.0(20): 0.793 Sensitivity CentroidAlifold(20): 0.732 PETfold_pre2.0(20): 0.776 Positive Predictive Value CentroidAlifold(20): 0.874 PETfold_pre2.0(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.75960267492e-05	19 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.858 PETfold_pre2.0(20): 0.796 Sensitivity PETfold_pre2.0(seed): 0.820 PETfold_pre2.0(20): 0.768 Positive Predictive Value PETfold_pre2.0(seed): 0.898 PETfold_pre2.0(20): 0.827 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	18 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 ContextFold: 0.748 Sensitivity PETfold_pre2.0(20): 0.776 ContextFold: 0.730 Positive Predictive Value PETfold_pre2.0(20): 0.815 ContextFold: 0.772 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	17 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.789 MXScarna(seed): 0.730 Sensitivity PETfold_pre2.0(20): 0.770 MXScarna(seed): 0.691 Positive Predictive Value PETfold_pre2.0(20): 0.813 MXScarna(seed): 0.777 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	18 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAalifold(20): 0.761 Sensitivity PETfold_pre2.0(20): 0.776 RNAalifold(20): 0.714 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08		+ PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 PPfold(20): 0.783 Sensitivity PETfold_pre2.0(20): 0.768 PPfold(20): 0.749 Positive Predictive Value PETfold_pre2.0(20): 0.808 PPfold(20): 0.823 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000165470040626	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 IPknot: 0.612 Sensitivity PETfold_pre2.0(20): 0.776 IPknot: 0.616 Positive Predictive Value PETfold_pre2.0(20): 0.815 IPknot: 0.617 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 MXScarna(20): 0.697 Sensitivity PETfold_pre2.0(20): 0.776 MXScarna(20): 0.680 Positive Predictive Value PETfold_pre2.0(20): 0.815 MXScarna(20): 0.721 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNASampler(20): 0.689 Sensitivity PETfold_pre2.0(20): 0.776 RNASampler(20): 0.643 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNASampler(20): 0.745 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 TurboFold(20): 0.742 Sensitivity PETfold_pre2.0(20): 0.768 TurboFold(20): 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.808 TurboFold(20): 0.753 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 CentroidAlifold(seed): 0.650 Sensitivity PETfold_pre2.0(20): 0.776 CentroidAlifold(seed): 0.449 Positive Predictive Value PETfold_pre2.0(20): 0.815 CentroidAlifold(seed): 0.947 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48104284388e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 CentroidFold: 0.644 Sensitivity PETfold_pre2.0(20): 0.776 CentroidFold: 0.652 Positive Predictive Value PETfold_pre2.0(20): 0.815 CentroidFold: 0.643 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Sfold: 0.623 Sensitivity PETfold_pre2.0(20): 0.776 Sfold: 0.622 Positive Predictive Value PETfold_pre2.0(20): 0.815 Sfold: 0.631 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 CentroidHomfold‑LAST: 0.697 Sensitivity PETfold_pre2.0(20): 0.814 CentroidHomfold‑LAST: 0.706 Positive Predictive Value PETfold_pre2.0(20): 0.847 CentroidHomfold‑LAST: 0.694 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Contrafold: 0.627 Sensitivity PETfold_pre2.0(20): 0.776 Contrafold: 0.657 Positive Predictive Value PETfold_pre2.0(20): 0.815 Contrafold: 0.607 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.643 PETfold_pre2.0(20): 0.547 Sensitivity RNAalifold(seed): 0.416 PETfold_pre2.0(20): 0.518 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.585 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 MaxExpect: 0.592 Sensitivity PETfold_pre2.0(20): 0.776 MaxExpect: 0.609 Positive Predictive Value PETfold_pre2.0(20): 0.815 MaxExpect: 0.585 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 HotKnots: 0.588 Sensitivity PETfold_pre2.0(20): 0.776 HotKnots: 0.634 Positive Predictive Value PETfold_pre2.0(20): 0.815 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 UNAFold: 0.572 Sensitivity PETfold_pre2.0(20): 0.776 UNAFold: 0.606 Positive Predictive Value PETfold_pre2.0(20): 0.815 UNAFold: 0.549 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 ProbKnot: 0.596 Sensitivity PETfold_pre2.0(20): 0.776 ProbKnot: 0.627 Positive Predictive Value PETfold_pre2.0(20): 0.815 ProbKnot: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Murlet(20): 0.682 Sensitivity PETfold_pre2.0(20): 0.776 Murlet(20): 0.611 Positive Predictive Value PETfold_pre2.0(20): 0.815 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 PknotsRG: 0.641 Sensitivity PETfold_pre2.0(20): 0.776 PknotsRG: 0.689 Positive Predictive Value PETfold_pre2.0(20): 0.815 PknotsRG: 0.604 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAfold: 0.600 Sensitivity PETfold_pre2.0(20): 0.776 RNAfold: 0.636 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAfold: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAshapes: 0.564 Sensitivity PETfold_pre2.0(20): 0.776 RNAshapes: 0.600 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Fold: 0.564 Sensitivity PETfold_pre2.0(20): 0.776 Fold: 0.606 Positive Predictive Value PETfold_pre2.0(20): 0.815 Fold: 0.534 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.600 TurboFold(seed): 0.546 Sensitivity PETfold_pre2.0(20): 0.575 TurboFold(seed): 0.553 Positive Predictive Value PETfold_pre2.0(20): 0.632 TurboFold(seed): 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.640 Afold: 0.516 Sensitivity PETfold_pre2.0(20): 0.612 Afold: 0.565 Positive Predictive Value PETfold_pre2.0(20): 0.675 Afold: 0.480 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Carnac(20): 0.665 Sensitivity PETfold_pre2.0(20): 0.776 Carnac(20): 0.515 Positive Predictive Value PETfold_pre2.0(20): 0.815 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 RSpredict(20): 0.625 Sensitivity PETfold_pre2.0(20): 0.763 RSpredict(20): 0.568 Positive Predictive Value PETfold_pre2.0(20): 0.823 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAsubopt: 0.627 Sensitivity PETfold_pre2.0(20): 0.776 RNAsubopt: 0.675 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAsubopt: 0.590 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.882 Cylofold: 0.728 Sensitivity PETfold_pre2.0(20): 0.846 Cylofold: 0.726 Positive Predictive Value PETfold_pre2.0(20): 0.924 Cylofold: 0.737 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 McQFold: 0.539 Sensitivity PETfold_pre2.0(20): 0.776 McQFold: 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.815 McQFold: 0.526 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNASLOpt: 0.559 Sensitivity PETfold_pre2.0(20): 0.776 RNASLOpt: 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNASLOpt: 0.566 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Pknots: 0.466 Sensitivity PETfold_pre2.0(20): 0.776 Pknots: 0.510 Positive Predictive Value PETfold_pre2.0(20): 0.815 Pknots: 0.437 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CRWrnafold: 0.663 Sensitivity PETfold_pre2.0(20): 0.707 CRWrnafold: 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 CRWrnafold: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.823 Multilign(20): 0.620 Sensitivity PETfold_pre2.0(20): 0.808 Multilign(20): 0.619 Positive Predictive Value PETfold_pre2.0(20): 0.842 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.43573297697e-08	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.367 PETfold_pre2.0(20): 0.316 Sensitivity RNASampler(seed): 0.349 PETfold_pre2.0(20): 0.313 Positive Predictive Value RNASampler(seed): 0.392 PETfold_pre2.0(20): 0.325 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Mastr(20): 0.577 Sensitivity PETfold_pre2.0(20): 0.776 Mastr(20): 0.471 Positive Predictive Value PETfold_pre2.0(20): 0.815 Mastr(20): 0.715 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Vsfold4: 0.506 Sensitivity PETfold_pre2.0(20): 0.814 Vsfold4: 0.507 Positive Predictive Value PETfold_pre2.0(20): 0.847 Vsfold4: 0.515 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.547 Murlet(seed): 0.515 Sensitivity PETfold_pre2.0(20): 0.518 Murlet(seed): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.585 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 MCFold: 0.483 Sensitivity PETfold_pre2.0(20): 0.751 MCFold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.788 MCFold: 0.439 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Vsfold5: 0.451 Sensitivity PETfold_pre2.0(20): 0.814 Vsfold5: 0.468 Positive Predictive Value PETfold_pre2.0(20): 0.847 Vsfold5: 0.447 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAwolf: 0.392 Sensitivity PETfold_pre2.0(20): 0.776 RNAwolf: 0.410 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 CMfinder(20): 0.648 Sensitivity PETfold_pre2.0(20): 0.846 CMfinder(20): 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.855 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.823 NanoFolder: 0.322 Sensitivity PETfold_pre2.0(20): 0.816 NanoFolder: 0.414 Positive Predictive Value PETfold_pre2.0(20): 0.833 NanoFolder: 0.264 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.826 RDfolder: 0.595 Sensitivity PETfold_pre2.0(20): 0.778 RDfolder: 0.545 Positive Predictive Value PETfold_pre2.0(20): 0.885 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 RSpredict(seed): 0.365 Sensitivity PETfold_pre2.0(20): 0.763 RSpredict(seed): 0.220 Positive Predictive Value PETfold_pre2.0(20): 0.823 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.553 Multilign(seed): 0.517 Sensitivity PETfold_pre2.0(20): 0.521 Multilign(seed): 0.479 Positive Predictive Value PETfold_pre2.0(20): 0.594 Multilign(seed): 0.565 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 PPfold(seed): 0.058 Sensitivity PETfold_pre2.0(20): 0.768 PPfold(seed): 0.012 Positive Predictive Value PETfold_pre2.0(20): 0.808 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.633 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.606 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.668 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.776 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.815 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.42071836373e-08	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.905 PETfold_2.0(seed): 0.905 Sensitivity PETfold_pre2.0(20): 0.889 PETfold_2.0(seed): 0.889 Positive Predictive Value PETfold_pre2.0(20): 0.923 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.905 PETfold_2.0(20): 0.905 Sensitivity PETfold_pre2.0(20): 0.889 PETfold_2.0(20): 0.889 Positive Predictive Value PETfold_pre2.0(20): 0.923 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PPfold(20)	21 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.802 PPfold(20): 0.793 Sensitivity CentroidAlifold(20): 0.734 PPfold(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.880 PPfold(20): 0.841 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 6.38150542963e-08	17 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.886 PPfold(20): 0.783 Sensitivity PETfold_pre2.0(seed): 0.856 PPfold(20): 0.749 Positive Predictive Value PETfold_pre2.0(seed): 0.919 PPfold(20): 0.823 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	11 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.802 ContextFold: 0.781 Sensitivity PPfold(20): 0.749 ContextFold: 0.731 Positive Predictive Value PPfold(20): 0.864 ContextFold: 0.840 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.65163701526e-08	15 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.812 MXScarna(seed): 0.736 Sensitivity PPfold(20): 0.753 MXScarna(seed): 0.688 Positive Predictive Value PPfold(20): 0.880 MXScarna(seed): 0.794 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.45096400029e-08	15 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.812 RNAalifold(20): 0.771 Sensitivity PPfold(20): 0.753 RNAalifold(20): 0.710 Positive Predictive Value PPfold(20): 0.880 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	17 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 PPfold(20): 0.783 Sensitivity PETfold_pre2.0(20): 0.768 PPfold(20): 0.749 Positive Predictive Value PETfold_pre2.0(20): 0.808 PPfold(20): 0.823 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000165470040626		+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.819 IPknot: 0.712 Sensitivity PPfold(20): 0.766 IPknot: 0.678 Positive Predictive Value PPfold(20): 0.879 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.812 MXScarna(20): 0.709 Sensitivity PPfold(20): 0.753 MXScarna(20): 0.669 Positive Predictive Value PPfold(20): 0.880 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.812 RNASampler(20): 0.741 Sensitivity PPfold(20): 0.753 RNASampler(20): 0.669 Positive Predictive Value PPfold(20): 0.880 RNASampler(20): 0.826 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.812 TurboFold(20): 0.773 Sensitivity PPfold(20): 0.753 TurboFold(20): 0.737 Positive Predictive Value PPfold(20): 0.880 TurboFold(20): 0.817 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.793 CentroidAlifold(seed): 0.667 Sensitivity PPfold(20): 0.752 CentroidAlifold(seed): 0.480 Positive Predictive Value PPfold(20): 0.841 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.793 CentroidFold: 0.671 Sensitivity PPfold(20): 0.752 CentroidFold: 0.674 Positive Predictive Value PPfold(20): 0.841 CentroidFold: 0.675 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.812 Sfold: 0.703 Sensitivity PPfold(20): 0.753 Sfold: 0.675 Positive Predictive Value PPfold(20): 0.880 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.18011954625e-08	+ PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.844 CentroidHomfold‑LAST: 0.760 Sensitivity PPfold(20): 0.791 CentroidHomfold‑LAST: 0.744 Positive Predictive Value PPfold(20): 0.906 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.812 Contrafold: 0.701 Sensitivity PPfold(20): 0.753 Contrafold: 0.702 Positive Predictive Value PPfold(20): 0.880 Contrafold: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	? RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.683 PPfold(20): 0.681 Sensitivity RNAalifold(seed): 0.502 PPfold(20): 0.596 Positive Predictive Value RNAalifold(seed): 0.936 PPfold(20): 0.786 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): 0.812 MaxExpect: 0.666 Sensitivity PPfold(20): 0.753 MaxExpect: 0.656 Positive Predictive Value PPfold(20): 0.880 MaxExpect: 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.812 HotKnots: 0.661 Sensitivity PPfold(20): 0.753 HotKnots: 0.686 Positive Predictive Value PPfold(20): 0.880 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.812 UNAFold: 0.661 Sensitivity PPfold(20): 0.753 UNAFold: 0.672 Positive Predictive Value PPfold(20): 0.880 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.812 ProbKnot: 0.670 Sensitivity PPfold(20): 0.753 ProbKnot: 0.686 Positive Predictive Value PPfold(20): 0.880 ProbKnot: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.812 Murlet(20): 0.663 Sensitivity PPfold(20): 0.753 Murlet(20): 0.593 Positive Predictive Value PPfold(20): 0.880 Murlet(20): 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.812 PknotsRG: 0.696 Sensitivity PPfold(20): 0.753 PknotsRG: 0.718 Positive Predictive Value PPfold(20): 0.880 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.812 RNAfold: 0.674 Sensitivity PPfold(20): 0.753 RNAfold: 0.686 Positive Predictive Value PPfold(20): 0.880 RNAfold: 0.671 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.812 RNAshapes: 0.669 Sensitivity PPfold(20): 0.753 RNAshapes: 0.678 Positive Predictive Value PPfold(20): 0.880 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.812 Fold: 0.634 Sensitivity PPfold(20): 0.753 Fold: 0.656 Positive Predictive Value PPfold(20): 0.880 Fold: 0.622 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.710 TurboFold(seed): 0.683 Sensitivity PPfold(20): 0.634 TurboFold(seed): 0.653 Positive Predictive Value PPfold(20): 0.801 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.718 Afold: 0.713 Sensitivity PPfold(20): 0.643 Afold: 0.723 Positive Predictive Value PPfold(20): 0.809 Afold: 0.711 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.812 Carnac(20): 0.638 Sensitivity PPfold(20): 0.753 Carnac(20): 0.491 Positive Predictive Value PPfold(20): 0.880 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.793 RSpredict(20): 0.624 Sensitivity PPfold(20): 0.752 RSpredict(20): 0.572 Positive Predictive Value PPfold(20): 0.841 RSpredict(20): 0.689 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.812 RNAsubopt: 0.672 Sensitivity PPfold(20): 0.753 RNAsubopt: 0.688 Positive Predictive Value PPfold(20): 0.880 RNAsubopt: 0.665 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.873 Cylofold: 0.768 Sensitivity PPfold(20): 0.813 Cylofold: 0.753 Positive Predictive Value PPfold(20): 0.943 Cylofold: 0.792 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.19192530585e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.812 McQFold: 0.680 Sensitivity PPfold(20): 0.753 McQFold: 0.678 Positive Predictive Value PPfold(20): 0.880 McQFold: 0.691 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.802 RNASLOpt: 0.635 Sensitivity PPfold(20): 0.749 RNASLOpt: 0.616 Positive Predictive Value PPfold(20): 0.864 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.812 Pknots: 0.591 Sensitivity PPfold(20): 0.753 Pknots: 0.621 Positive Predictive Value PPfold(20): 0.880 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.780 CRWrnafold: 0.668 Sensitivity PPfold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value PPfold(20): 0.844 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.844 Multilign(20): 0.699 Sensitivity PPfold(20): 0.791 Multilign(20): 0.688 Positive Predictive Value PPfold(20): 0.906 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.39162260866e-08	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.617 PPfold(20): 0.609 Sensitivity RNASampler(seed): 0.525 PPfold(20): 0.533 Positive Predictive Value RNASampler(seed): 0.733 PPfold(20): 0.703 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.842 Alterna: 0.750 Sensitivity PPfold(20): 0.767 Alterna: 0.756 Positive Predictive Value PPfold(20): 0.932 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.812 Mastr(20): 0.631 Sensitivity PPfold(20): 0.753 Mastr(20): 0.509 Positive Predictive Value PPfold(20): 0.880 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.844 Vsfold4: 0.619 Sensitivity PPfold(20): 0.791 Vsfold4: 0.603 Positive Predictive Value PPfold(20): 0.906 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.681 Murlet(seed): 0.543 Sensitivity PPfold(20): 0.596 Murlet(seed): 0.360 Positive Predictive Value PPfold(20): 0.786 Murlet(seed): 0.830 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.778 MCFold: 0.518 Sensitivity PPfold(20): 0.736 MCFold: 0.574 Positive Predictive Value PPfold(20): 0.828 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.844 Vsfold5: 0.546 Sensitivity PPfold(20): 0.791 Vsfold5: 0.544 Positive Predictive Value PPfold(20): 0.906 Vsfold5: 0.561 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.798 RNAwolf: 0.429 Sensitivity PPfold(20): 0.761 RNAwolf: 0.446 Positive Predictive Value PPfold(20): 0.840 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.927 CMfinder(20): 0.652 Sensitivity PPfold(20): 0.895 CMfinder(20): 0.518 Positive Predictive Value PPfold(20): 0.962 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.848 NanoFolder: 0.329 Sensitivity PPfold(20): 0.816 NanoFolder: 0.405 Positive Predictive Value PPfold(20): 0.886 NanoFolder: 0.283 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): 0.829 RDfolder: 0.584 Sensitivity PPfold(20): 0.753 RDfolder: 0.518 Positive Predictive Value PPfold(20): 0.921 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.793 RSpredict(seed): 0.180 Sensitivity PPfold(20): 0.752 RSpredict(seed): 0.086 Positive Predictive Value PPfold(20): 0.841 RSpredict(seed): 0.394 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.81788725234e-08	? Multilign(seed) vs PPfold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 PPfold(20): 0.728 Sensitivity Multilign(seed): 0.682 PPfold(20): 0.643 Positive Predictive Value Multilign(seed): 0.793 PPfold(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.819 PPfold(seed): 0.046 Sensitivity PPfold(20): 0.766 PPfold(seed): 0.009 Positive Predictive Value PPfold(20): 0.879 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.723 Carnac(seed): 0.272 Sensitivity PPfold(20): 0.646 Carnac(seed): 0.075 Positive Predictive Value PPfold(20): 0.816 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.10032755566e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.812 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.753 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.880 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.64481516727e-08	? PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
IPknot	21 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.812 IPknot: 0.639 Sensitivity CentroidAlifold(20): 0.745 IPknot: 0.637 Positive Predictive Value CentroidAlifold(20): 0.890 IPknot: 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 IPknot: 0.710 Sensitivity PETfold_pre2.0(seed): 0.841 IPknot: 0.700 Positive Predictive Value PETfold_pre2.0(seed): 0.892 IPknot: 0.722 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.680 IPknot: 0.663 Sensitivity ContextFold: 0.671 IPknot: 0.633 Positive Predictive Value ContextFold: 0.689 IPknot: 0.695 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 5.84585956207e-05	20 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.781 IPknot: 0.745 Sensitivity MXScarna(seed): 0.745 IPknot: 0.717 Positive Predictive Value MXScarna(seed): 0.819 IPknot: 0.775 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.00017354801e-07	14 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.784 IPknot: 0.712 Sensitivity RNAalifold(20): 0.721 IPknot: 0.678 Positive Predictive Value RNAalifold(20): 0.858 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	18 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 IPknot: 0.612 Sensitivity PETfold_pre2.0(20): 0.776 IPknot: 0.616 Positive Predictive Value PETfold_pre2.0(20): 0.815 IPknot: 0.617 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	14 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.819 IPknot: 0.712 Sensitivity PPfold(20): 0.766 IPknot: 0.678 Positive Predictive Value PPfold(20): 0.879 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08		= IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.712 MXScarna(20): 0.707 Sensitivity IPknot: 0.678 MXScarna(20): 0.667 Positive Predictive Value IPknot: 0.756 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00187401051877	- RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.729 IPknot: 0.712 Sensitivity RNASampler(20): 0.655 IPknot: 0.678 Positive Predictive Value RNASampler(20): 0.819 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10678710489e-07	- TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.764 IPknot: 0.712 Sensitivity TurboFold(20): 0.726 IPknot: 0.678 Positive Predictive Value TurboFold(20): 0.810 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	- CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.764 IPknot: 0.717 Sensitivity CentroidAlifold(seed): 0.627 IPknot: 0.704 Positive Predictive Value CentroidAlifold(seed): 0.932 IPknot: 0.731 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.57333037898e-08	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.669 CentroidFold: 0.627 Sensitivity IPknot: 0.645 CentroidFold: 0.613 Positive Predictive Value IPknot: 0.695 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.675 Sfold: 0.604 Sensitivity IPknot: 0.645 Sfold: 0.607 Positive Predictive Value IPknot: 0.707 Sfold: 0.603 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.760 CentroidHomfold‑LAST: 0.704 Sensitivity IPknot: 0.747 CentroidHomfold‑LAST: 0.628 Positive Predictive Value IPknot: 0.777 CentroidHomfold‑LAST: 0.794 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.675 Contrafold: 0.607 Sensitivity IPknot: 0.645 Contrafold: 0.621 Positive Predictive Value IPknot: 0.707 Contrafold: 0.594 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.781 IPknot: 0.721 Sensitivity RNAalifold(seed): 0.701 IPknot: 0.689 Positive Predictive Value RNAalifold(seed): 0.870 IPknot: 0.754 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.675 MaxExpect: 0.583 Sensitivity IPknot: 0.645 MaxExpect: 0.600 Positive Predictive Value IPknot: 0.707 MaxExpect: 0.569 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.742 HotKnots: 0.673 Sensitivity IPknot: 0.729 HotKnots: 0.700 Positive Predictive Value IPknot: 0.759 HotKnots: 0.654 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.675 UNAFold: 0.576 Sensitivity IPknot: 0.645 UNAFold: 0.600 Positive Predictive Value IPknot: 0.707 UNAFold: 0.554 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.675 ProbKnot: 0.579 Sensitivity IPknot: 0.645 ProbKnot: 0.604 Positive Predictive Value IPknot: 0.707 ProbKnot: 0.557 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.712 Murlet(20): 0.671 Sensitivity IPknot: 0.678 Murlet(20): 0.598 Positive Predictive Value IPknot: 0.756 Murlet(20): 0.761 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.652 PknotsRG: 0.588 Sensitivity IPknot: 0.617 PknotsRG: 0.623 Positive Predictive Value IPknot: 0.691 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.675 RNAfold: 0.578 Sensitivity IPknot: 0.645 RNAfold: 0.604 Positive Predictive Value IPknot: 0.707 RNAfold: 0.555 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.742 RNAshapes: 0.633 Sensitivity IPknot: 0.729 RNAshapes: 0.653 Positive Predictive Value IPknot: 0.759 RNAshapes: 0.621 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.675 Fold: 0.542 Sensitivity IPknot: 0.645 Fold: 0.574 Positive Predictive Value IPknot: 0.707 Fold: 0.513 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.650 TurboFold(seed): 0.624 Sensitivity IPknot: 0.590 TurboFold(seed): 0.590 Positive Predictive Value IPknot: 0.724 TurboFold(seed): 0.670 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.35010831363e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.598 Afold: 0.528 Sensitivity IPknot: 0.559 Afold: 0.566 Positive Predictive Value IPknot: 0.642 Afold: 0.495 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.712 Carnac(20): 0.654 Sensitivity IPknot: 0.678 Carnac(20): 0.516 Positive Predictive Value IPknot: 0.756 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.645 RSpredict(20): 0.627 Sensitivity IPknot: 0.641 RSpredict(20): 0.575 Positive Predictive Value IPknot: 0.656 RSpredict(20): 0.693 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 7.4038562879e-07	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.742 RNAsubopt: 0.630 Sensitivity IPknot: 0.729 RNAsubopt: 0.663 Positive Predictive Value IPknot: 0.759 RNAsubopt: 0.606 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.753 Cylofold: 0.626 Sensitivity IPknot: 0.733 Cylofold: 0.615 Positive Predictive Value IPknot: 0.780 Cylofold: 0.649 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.672 McQFold: 0.491 Sensitivity IPknot: 0.642 McQFold: 0.503 Positive Predictive Value IPknot: 0.705 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.729 RNASLOpt: 0.580 Sensitivity IPknot: 0.718 RNASLOpt: 0.559 Positive Predictive Value IPknot: 0.744 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.768 Pknots: 0.606 Sensitivity IPknot: 0.746 Pknots: 0.634 Positive Predictive Value IPknot: 0.798 Pknots: 0.590 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.757 CRWrnafold: 0.683 Sensitivity IPknot: 0.731 CRWrnafold: 0.690 Positive Predictive Value IPknot: 0.793 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.727 Multilign(20): 0.681 Sensitivity IPknot: 0.708 Multilign(20): 0.671 Positive Predictive Value IPknot: 0.755 Multilign(20): 0.701 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.59816551561e-08	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.660 RNASampler(seed): 0.530 Sensitivity IPknot: 0.595 RNASampler(seed): 0.425 Positive Predictive Value IPknot: 0.740 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.791 Alterna: 0.684 Sensitivity IPknot: 0.754 Alterna: 0.705 Positive Predictive Value IPknot: 0.840 Alterna: 0.679 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.712 Mastr(20): 0.616 Sensitivity IPknot: 0.678 Mastr(20): 0.493 Positive Predictive Value IPknot: 0.756 Mastr(20): 0.779 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.764 Vsfold4: 0.590 Sensitivity IPknot: 0.751 Vsfold4: 0.580 Positive Predictive Value IPknot: 0.783 Vsfold4: 0.611 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.670 Murlet(seed): 0.496 Sensitivity IPknot: 0.610 Murlet(seed): 0.337 Positive Predictive Value IPknot: 0.745 Murlet(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.4651262096e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.724 MCFold: 0.550 Sensitivity IPknot: 0.713 MCFold: 0.586 Positive Predictive Value IPknot: 0.743 MCFold: 0.528 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.753 Vsfold5: 0.523 Sensitivity IPknot: 0.737 Vsfold5: 0.531 Positive Predictive Value IPknot: 0.777 Vsfold5: 0.529 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.669 RNAwolf: 0.436 Sensitivity IPknot: 0.645 RNAwolf: 0.446 Positive Predictive Value IPknot: 0.695 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.749 CMfinder(20): 0.652 Sensitivity IPknot: 0.746 CMfinder(20): 0.518 Positive Predictive Value IPknot: 0.759 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.750 NanoFolder: 0.394 Sensitivity IPknot: 0.749 NanoFolder: 0.485 Positive Predictive Value IPknot: 0.758 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.756 RDfolder: 0.568 Sensitivity IPknot: 0.728 RDfolder: 0.514 Positive Predictive Value IPknot: 0.797 RDfolder: 0.648 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.721 RSpredict(seed): 0.478 Sensitivity IPknot: 0.708 RSpredict(seed): 0.346 Positive Predictive Value IPknot: 0.736 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.710 Multilign(seed): 0.617 Sensitivity IPknot: 0.632 Multilign(seed): 0.558 Positive Predictive Value IPknot: 0.805 Multilign(seed): 0.693 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.739 PPfold(seed): 0.094 Sensitivity IPknot: 0.696 PPfold(seed): 0.019 Positive Predictive Value IPknot: 0.791 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.726 Carnac(seed): 0.553 Sensitivity IPknot: 0.696 Carnac(seed): 0.330 Positive Predictive Value IPknot: 0.760 Carnac(seed): 0.929 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.739 Mastr(seed): 0.000 Sensitivity IPknot: 0.696 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.791 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	? CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 IPknot: 0.766 Sensitivity PETfold_2.0(seed): 0.845 IPknot: 0.776 Positive Predictive Value PETfold_2.0(seed): 0.891 IPknot: 0.763 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.905 IPknot: 0.541 Sensitivity PETfold_2.0(20): 0.889 IPknot: 0.556 Positive Predictive Value PETfold_2.0(20): 0.923 IPknot: 0.536 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MXScarna(20)	39 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 MXScarna(20): 0.749 Sensitivity CentroidAlifold(20): 0.728 MXScarna(20): 0.724 Positive Predictive Value CentroidAlifold(20): 0.901 MXScarna(20): 0.780 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 MXScarna(20): 0.697 Sensitivity PETfold_pre2.0(seed): 0.858 MXScarna(20): 0.680 Positive Predictive Value PETfold_pre2.0(seed): 0.919 MXScarna(20): 0.721 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	11 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.781 MXScarna(20): 0.670 Sensitivity ContextFold: 0.731 MXScarna(20): 0.627 Positive Predictive Value ContextFold: 0.840 MXScarna(20): 0.723 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.07229227445e-09	33 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 MXScarna(20): 0.754 Sensitivity MXScarna(seed): 0.732 MXScarna(20): 0.718 Positive Predictive Value MXScarna(seed): 0.825 MXScarna(20): 0.796 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 MXScarna(20): 0.755 Sensitivity RNAalifold(20): 0.704 MXScarna(20): 0.720 Positive Predictive Value RNAalifold(20): 0.891 MXScarna(20): 0.796 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 MXScarna(20): 0.697 Sensitivity PETfold_pre2.0(20): 0.776 MXScarna(20): 0.680 Positive Predictive Value PETfold_pre2.0(20): 0.815 MXScarna(20): 0.721 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	15 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.812 MXScarna(20): 0.709 Sensitivity PPfold(20): 0.753 MXScarna(20): 0.669 Positive Predictive Value PPfold(20): 0.880 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	14 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.712 MXScarna(20): 0.707 Sensitivity IPknot: 0.678 MXScarna(20): 0.667 Positive Predictive Value IPknot: 0.756 MXScarna(20): 0.757 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00187401051877		+ MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.755 RNASampler(20): 0.751 Sensitivity MXScarna(20): 0.720 RNASampler(20): 0.663 Positive Predictive Value MXScarna(20): 0.796 RNASampler(20): 0.856 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.000114481332584	- TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.773 MXScarna(20): 0.709 Sensitivity TurboFold(20): 0.737 MXScarna(20): 0.669 Positive Predictive Value TurboFold(20): 0.817 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 CentroidAlifold(seed): 0.695 Sensitivity MXScarna(20): 0.724 CentroidAlifold(seed): 0.528 Positive Predictive Value MXScarna(20): 0.780 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.749 CentroidFold: 0.690 Sensitivity MXScarna(20): 0.724 CentroidFold: 0.689 Positive Predictive Value MXScarna(20): 0.780 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.755 Sfold: 0.707 Sensitivity MXScarna(20): 0.720 Sfold: 0.683 Positive Predictive Value MXScarna(20): 0.796 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 MXScarna(20): 0.737 Sensitivity CentroidHomfold‑LAST: 0.744 MXScarna(20): 0.700 Positive Predictive Value CentroidHomfold‑LAST: 0.783 MXScarna(20): 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.97503173922e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.755 Contrafold: 0.664 Sensitivity MXScarna(20): 0.720 Contrafold: 0.681 Positive Predictive Value MXScarna(20): 0.796 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 RNAalifold(seed): 0.672 Sensitivity MXScarna(20): 0.644 RNAalifold(seed): 0.488 Positive Predictive Value MXScarna(20): 0.741 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.19220141104e-07	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.751 MaxExpect: 0.690 Sensitivity MXScarna(20): 0.715 MaxExpect: 0.693 Positive Predictive Value MXScarna(20): 0.794 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.755 HotKnots: 0.668 Sensitivity MXScarna(20): 0.720 HotKnots: 0.692 Positive Predictive Value MXScarna(20): 0.796 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.755 UNAFold: 0.692 Sensitivity MXScarna(20): 0.720 UNAFold: 0.701 Positive Predictive Value MXScarna(20): 0.796 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.736 ProbKnot: 0.679 Sensitivity MXScarna(20): 0.697 ProbKnot: 0.700 Positive Predictive Value MXScarna(20): 0.782 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Murlet(20): 0.693 Sensitivity MXScarna(20): 0.720 Murlet(20): 0.594 Positive Predictive Value MXScarna(20): 0.796 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.755 PknotsRG: 0.687 Sensitivity MXScarna(20): 0.720 PknotsRG: 0.709 Positive Predictive Value MXScarna(20): 0.796 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.755 RNAfold: 0.677 Sensitivity MXScarna(20): 0.720 RNAfold: 0.694 Positive Predictive Value MXScarna(20): 0.796 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.755 RNAshapes: 0.685 Sensitivity MXScarna(20): 0.720 RNAshapes: 0.694 Positive Predictive Value MXScarna(20): 0.796 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.736 Fold: 0.694 Sensitivity MXScarna(20): 0.697 Fold: 0.715 Positive Predictive Value MXScarna(20): 0.782 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 MXScarna(20): 0.621 Sensitivity TurboFold(seed): 0.653 MXScarna(20): 0.579 Positive Predictive Value TurboFold(seed): 0.723 MXScarna(20): 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.746 Afold: 0.639 Sensitivity MXScarna(20): 0.715 Afold: 0.658 Positive Predictive Value MXScarna(20): 0.783 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Carnac(20): 0.686 Sensitivity MXScarna(20): 0.720 Carnac(20): 0.518 Positive Predictive Value MXScarna(20): 0.796 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.745 RSpredict(20): 0.660 Sensitivity MXScarna(20): 0.719 RSpredict(20): 0.597 Positive Predictive Value MXScarna(20): 0.776 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.755 RNAsubopt: 0.660 Sensitivity MXScarna(20): 0.720 RNAsubopt: 0.684 Positive Predictive Value MXScarna(20): 0.796 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.804 Cylofold: 0.715 Sensitivity MXScarna(20): 0.760 Cylofold: 0.713 Positive Predictive Value MXScarna(20): 0.855 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.755 McQFold: 0.641 Sensitivity MXScarna(20): 0.720 McQFold: 0.648 Positive Predictive Value MXScarna(20): 0.796 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.670 RNASLOpt: 0.635 Sensitivity MXScarna(20): 0.627 RNASLOpt: 0.616 Positive Predictive Value MXScarna(20): 0.723 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.89166989468e-09	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.775 Pknots: 0.619 Sensitivity MXScarna(20): 0.742 Pknots: 0.663 Positive Predictive Value MXScarna(20): 0.815 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.668 MXScarna(20): 0.666 Sensitivity CRWrnafold: 0.683 MXScarna(20): 0.634 Positive Predictive Value CRWrnafold: 0.663 MXScarna(20): 0.707 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.750 Multilign(20): 0.652 Sensitivity MXScarna(20): 0.715 Multilign(20): 0.624 Positive Predictive Value MXScarna(20): 0.795 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 MXScarna(20): 0.640 Sensitivity RNASampler(seed): 0.604 MXScarna(20): 0.626 Positive Predictive Value RNASampler(seed): 0.748 MXScarna(20): 0.661 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.846 Alterna: 0.671 Sensitivity MXScarna(20): 0.803 Alterna: 0.680 Positive Predictive Value MXScarna(20): 0.897 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Mastr(20): 0.620 Sensitivity MXScarna(20): 0.720 Mastr(20): 0.473 Positive Predictive Value MXScarna(20): 0.796 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.767 Vsfold4: 0.561 Sensitivity MXScarna(20): 0.734 Vsfold4: 0.556 Positive Predictive Value MXScarna(20): 0.807 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.711 Murlet(seed): 0.557 Sensitivity MXScarna(20): 0.667 Murlet(seed): 0.355 Positive Predictive Value MXScarna(20): 0.764 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.758 MCFold: 0.499 Sensitivity MXScarna(20): 0.735 MCFold: 0.560 Positive Predictive Value MXScarna(20): 0.787 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.767 Vsfold5: 0.494 Sensitivity MXScarna(20): 0.734 Vsfold5: 0.496 Positive Predictive Value MXScarna(20): 0.807 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.718 RNAwolf: 0.438 Sensitivity MXScarna(20): 0.699 RNAwolf: 0.454 Positive Predictive Value MXScarna(20): 0.743 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.772 CMfinder(20): 0.652 Sensitivity MXScarna(20): 0.737 CMfinder(20): 0.518 Positive Predictive Value MXScarna(20): 0.816 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.709 NanoFolder: 0.329 Sensitivity MXScarna(20): 0.689 NanoFolder: 0.405 Positive Predictive Value MXScarna(20): 0.736 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.812 RDfolder: 0.636 Sensitivity MXScarna(20): 0.755 RDfolder: 0.602 Positive Predictive Value MXScarna(20): 0.880 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.745 RSpredict(seed): 0.230 Sensitivity MXScarna(20): 0.719 RSpredict(seed): 0.114 Positive Predictive Value MXScarna(20): 0.776 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.732 MXScarna(20): 0.666 Sensitivity Multilign(seed): 0.682 MXScarna(20): 0.636 Positive Predictive Value Multilign(seed): 0.793 MXScarna(20): 0.707 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.707 PPfold(seed): 0.046 Sensitivity MXScarna(20): 0.667 PPfold(seed): 0.009 Positive Predictive Value MXScarna(20): 0.757 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.739 Carnac(seed): 0.220 Sensitivity MXScarna(20): 0.702 Carnac(seed): 0.049 Positive Predictive Value MXScarna(20): 0.784 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.755 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.720 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient MXScarna(20): 1.000 PETfold_2.0(seed): 0.905 Sensitivity MXScarna(20): 1.000 PETfold_2.0(seed): 0.889 Positive Predictive Value MXScarna(20): 1.000 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 1.000 PETfold_2.0(20): 0.905 Sensitivity MXScarna(20): 1.000 PETfold_2.0(20): 0.889 Positive Predictive Value MXScarna(20): 1.000 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASampler(20)	39 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNASampler(20): 0.738 Sensitivity CentroidAlifold(20): 0.728 RNASampler(20): 0.667 Positive Predictive Value CentroidAlifold(20): 0.901 RNASampler(20): 0.822 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 RNASampler(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.858 RNASampler(20): 0.643 Positive Predictive Value PETfold_pre2.0(seed): 0.919 RNASampler(20): 0.745 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	11 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.781 RNASampler(20): 0.690 Sensitivity ContextFold: 0.731 RNASampler(20): 0.616 Positive Predictive Value ContextFold: 0.840 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	33 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 RNASampler(20): 0.752 Sensitivity MXScarna(seed): 0.732 RNASampler(20): 0.667 Positive Predictive Value MXScarna(seed): 0.825 RNASampler(20): 0.853 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 1.00387151331e-07	34 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 RNASampler(20): 0.751 Sensitivity RNAalifold(20): 0.704 RNASampler(20): 0.663 Positive Predictive Value RNAalifold(20): 0.891 RNASampler(20): 0.856 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNASampler(20): 0.689 Sensitivity PETfold_pre2.0(20): 0.776 RNASampler(20): 0.643 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNASampler(20): 0.745 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	15 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.812 RNASampler(20): 0.741 Sensitivity PPfold(20): 0.753 RNASampler(20): 0.669 Positive Predictive Value PPfold(20): 0.880 RNASampler(20): 0.826 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	14 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.729 IPknot: 0.712 Sensitivity RNASampler(20): 0.655 IPknot: 0.678 Positive Predictive Value RNASampler(20): 0.819 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10678710489e-07	34 MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.755 RNASampler(20): 0.751 Sensitivity MXScarna(20): 0.720 RNASampler(20): 0.663 Positive Predictive Value MXScarna(20): 0.796 RNASampler(20): 0.856 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.000114481332584		- TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.773 RNASampler(20): 0.741 Sensitivity TurboFold(20): 0.737 RNASampler(20): 0.669 Positive Predictive Value TurboFold(20): 0.817 RNASampler(20): 0.826 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.23667249354e-08	+ RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.738 CentroidAlifold(seed): 0.695 Sensitivity RNASampler(20): 0.667 CentroidAlifold(seed): 0.528 Positive Predictive Value RNASampler(20): 0.822 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.738 CentroidFold: 0.690 Sensitivity RNASampler(20): 0.667 CentroidFold: 0.689 Positive Predictive Value RNASampler(20): 0.822 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.751 Sfold: 0.707 Sensitivity RNASampler(20): 0.663 Sfold: 0.683 Positive Predictive Value RNASampler(20): 0.856 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.774 CentroidHomfold‑LAST: 0.760 Sensitivity RNASampler(20): 0.700 CentroidHomfold‑LAST: 0.744 Positive Predictive Value RNASampler(20): 0.862 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.33374751016e-06	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.751 Contrafold: 0.664 Sensitivity RNASampler(20): 0.663 Contrafold: 0.681 Positive Predictive Value RNASampler(20): 0.856 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 RNASampler(20): 0.671 Sensitivity RNAalifold(seed): 0.488 RNASampler(20): 0.575 Positive Predictive Value RNAalifold(seed): 0.931 RNASampler(20): 0.789 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.000699240967729	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.749 MaxExpect: 0.690 Sensitivity RNASampler(20): 0.663 MaxExpect: 0.693 Positive Predictive Value RNASampler(20): 0.851 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.751 HotKnots: 0.668 Sensitivity RNASampler(20): 0.663 HotKnots: 0.692 Positive Predictive Value RNASampler(20): 0.856 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.751 UNAFold: 0.692 Sensitivity RNASampler(20): 0.663 UNAFold: 0.701 Positive Predictive Value RNASampler(20): 0.856 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.721 ProbKnot: 0.679 Sensitivity RNASampler(20): 0.625 ProbKnot: 0.700 Positive Predictive Value RNASampler(20): 0.837 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Murlet(20): 0.693 Sensitivity RNASampler(20): 0.663 Murlet(20): 0.594 Positive Predictive Value RNASampler(20): 0.856 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.751 PknotsRG: 0.687 Sensitivity RNASampler(20): 0.663 PknotsRG: 0.709 Positive Predictive Value RNASampler(20): 0.856 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.751 RNAfold: 0.677 Sensitivity RNASampler(20): 0.663 RNAfold: 0.694 Positive Predictive Value RNASampler(20): 0.856 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.751 RNAshapes: 0.685 Sensitivity RNASampler(20): 0.663 RNAshapes: 0.694 Positive Predictive Value RNASampler(20): 0.856 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.721 Fold: 0.694 Sensitivity RNASampler(20): 0.625 Fold: 0.715 Positive Predictive Value RNASampler(20): 0.837 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.705 TurboFold(seed): 0.683 Sensitivity RNASampler(20): 0.630 TurboFold(seed): 0.653 Positive Predictive Value RNASampler(20): 0.795 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.730 Afold: 0.639 Sensitivity RNASampler(20): 0.635 Afold: 0.658 Positive Predictive Value RNASampler(20): 0.844 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Carnac(20): 0.686 Sensitivity RNASampler(20): 0.663 Carnac(20): 0.518 Positive Predictive Value RNASampler(20): 0.856 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.737 RSpredict(20): 0.660 Sensitivity RNASampler(20): 0.667 RSpredict(20): 0.597 Positive Predictive Value RNASampler(20): 0.820 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.751 RNAsubopt: 0.660 Sensitivity RNASampler(20): 0.663 RNAsubopt: 0.684 Positive Predictive Value RNASampler(20): 0.856 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.789 Cylofold: 0.715 Sensitivity RNASampler(20): 0.691 Cylofold: 0.713 Positive Predictive Value RNASampler(20): 0.906 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.751 McQFold: 0.641 Sensitivity RNASampler(20): 0.663 McQFold: 0.648 Positive Predictive Value RNASampler(20): 0.856 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.690 RNASLOpt: 0.635 Sensitivity RNASampler(20): 0.616 RNASLOpt: 0.616 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.16131455263e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.777 Pknots: 0.619 Sensitivity RNASampler(20): 0.693 Pknots: 0.663 Positive Predictive Value RNASampler(20): 0.875 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.740 CRWrnafold: 0.668 Sensitivity RNASampler(20): 0.659 CRWrnafold: 0.683 Positive Predictive Value RNASampler(20): 0.837 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.744 Multilign(20): 0.652 Sensitivity RNASampler(20): 0.645 Multilign(20): 0.624 Positive Predictive Value RNASampler(20): 0.864 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	? RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 RNASampler(20): 0.666 Sensitivity RNASampler(seed): 0.604 RNASampler(20): 0.647 Positive Predictive Value RNASampler(seed): 0.748 RNASampler(20): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.912 Alterna: 0.671 Sensitivity RNASampler(20): 0.846 Alterna: 0.680 Positive Predictive Value RNASampler(20): 0.986 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Mastr(20): 0.620 Sensitivity RNASampler(20): 0.663 Mastr(20): 0.473 Positive Predictive Value RNASampler(20): 0.856 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold4: 0.561 Sensitivity RNASampler(20): 0.675 Vsfold4: 0.556 Positive Predictive Value RNASampler(20): 0.872 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.701 Murlet(seed): 0.557 Sensitivity RNASampler(20): 0.610 Murlet(seed): 0.355 Positive Predictive Value RNASampler(20): 0.813 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.754 MCFold: 0.499 Sensitivity RNASampler(20): 0.696 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.823 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold5: 0.494 Sensitivity RNASampler(20): 0.675 Vsfold5: 0.496 Positive Predictive Value RNASampler(20): 0.872 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.716 RNAwolf: 0.438 Sensitivity RNASampler(20): 0.666 RNAwolf: 0.454 Positive Predictive Value RNASampler(20): 0.776 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.721 CMfinder(20): 0.652 Sensitivity RNASampler(20): 0.640 CMfinder(20): 0.518 Positive Predictive Value RNASampler(20): 0.820 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.724 NanoFolder: 0.329 Sensitivity RNASampler(20): 0.653 NanoFolder: 0.405 Positive Predictive Value RNASampler(20): 0.810 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.883 RDfolder: 0.636 Sensitivity RNASampler(20): 0.805 RDfolder: 0.602 Positive Predictive Value RNASampler(20): 0.972 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.737 RSpredict(seed): 0.230 Sensitivity RNASampler(20): 0.667 RSpredict(seed): 0.114 Positive Predictive Value RNASampler(20): 0.820 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.732 RNASampler(20): 0.720 Sensitivity Multilign(seed): 0.682 RNASampler(20): 0.643 Positive Predictive Value Multilign(seed): 0.793 RNASampler(20): 0.814 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.729 PPfold(seed): 0.046 Sensitivity RNASampler(20): 0.655 PPfold(seed): 0.009 Positive Predictive Value RNASampler(20): 0.819 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.742 Carnac(seed): 0.220 Sensitivity RNASampler(20): 0.652 Carnac(seed): 0.049 Positive Predictive Value RNASampler(20): 0.850 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.751 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.663 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.856 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 RNASampler(20): 0.881 Sensitivity PETfold_2.0(seed): 0.889 RNASampler(20): 0.778 Positive Predictive Value PETfold_2.0(seed): 0.923 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNASampler(20): 0.881 Sensitivity PETfold_2.0(20): 0.889 RNASampler(20): 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
TurboFold(20)	21 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.802 TurboFold(20): 0.758 Sensitivity CentroidAlifold(20): 0.734 TurboFold(20): 0.748 Positive Predictive Value CentroidAlifold(20): 0.880 TurboFold(20): 0.773 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	17 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.886 TurboFold(20): 0.742 Sensitivity PETfold_pre2.0(seed): 0.856 TurboFold(20): 0.737 Positive Predictive Value PETfold_pre2.0(seed): 0.919 TurboFold(20): 0.753 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	11 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.781 TurboFold(20): 0.755 Sensitivity ContextFold: 0.731 TurboFold(20): 0.717 Positive Predictive Value ContextFold: 0.840 TurboFold(20): 0.800 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	15 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.773 MXScarna(seed): 0.736 Sensitivity TurboFold(20): 0.737 MXScarna(seed): 0.688 Positive Predictive Value TurboFold(20): 0.817 MXScarna(seed): 0.794 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	15 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.773 RNAalifold(20): 0.771 Sensitivity TurboFold(20): 0.737 RNAalifold(20): 0.710 Positive Predictive Value TurboFold(20): 0.817 RNAalifold(20): 0.842 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.149956528961	17 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 TurboFold(20): 0.742 Sensitivity PETfold_pre2.0(20): 0.768 TurboFold(20): 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.808 TurboFold(20): 0.753 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	15 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.812 TurboFold(20): 0.773 Sensitivity PPfold(20): 0.753 TurboFold(20): 0.737 Positive Predictive Value PPfold(20): 0.880 TurboFold(20): 0.817 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	14 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.764 IPknot: 0.712 Sensitivity TurboFold(20): 0.726 IPknot: 0.678 Positive Predictive Value TurboFold(20): 0.810 IPknot: 0.756 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	15 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.773 MXScarna(20): 0.709 Sensitivity TurboFold(20): 0.737 MXScarna(20): 0.669 Positive Predictive Value TurboFold(20): 0.817 MXScarna(20): 0.758 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	15 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.773 RNASampler(20): 0.741 Sensitivity TurboFold(20): 0.737 RNASampler(20): 0.669 Positive Predictive Value TurboFold(20): 0.817 RNASampler(20): 0.826 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.23667249354e-08		+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.758 CentroidAlifold(seed): 0.667 Sensitivity TurboFold(20): 0.748 CentroidAlifold(seed): 0.480 Positive Predictive Value TurboFold(20): 0.773 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.758 CentroidFold: 0.671 Sensitivity TurboFold(20): 0.748 CentroidFold: 0.674 Positive Predictive Value TurboFold(20): 0.773 CentroidFold: 0.675 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.773 Sfold: 0.703 Sensitivity TurboFold(20): 0.737 Sfold: 0.675 Positive Predictive Value TurboFold(20): 0.817 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.796 CentroidHomfold‑LAST: 0.760 Sensitivity TurboFold(20): 0.762 CentroidHomfold‑LAST: 0.744 Positive Predictive Value TurboFold(20): 0.838 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.36290909588e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.773 Contrafold: 0.701 Sensitivity TurboFold(20): 0.737 Contrafold: 0.702 Positive Predictive Value TurboFold(20): 0.817 Contrafold: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	? TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.691 RNAalifold(seed): 0.683 Sensitivity TurboFold(20): 0.645 RNAalifold(seed): 0.502 Positive Predictive Value TurboFold(20): 0.749 RNAalifold(seed): 0.936 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.773 MaxExpect: 0.666 Sensitivity TurboFold(20): 0.737 MaxExpect: 0.656 Positive Predictive Value TurboFold(20): 0.817 MaxExpect: 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.773 HotKnots: 0.661 Sensitivity TurboFold(20): 0.737 HotKnots: 0.686 Positive Predictive Value TurboFold(20): 0.817 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.773 UNAFold: 0.661 Sensitivity TurboFold(20): 0.737 UNAFold: 0.672 Positive Predictive Value TurboFold(20): 0.817 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.773 ProbKnot: 0.670 Sensitivity TurboFold(20): 0.737 ProbKnot: 0.686 Positive Predictive Value TurboFold(20): 0.817 ProbKnot: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.773 Murlet(20): 0.663 Sensitivity TurboFold(20): 0.737 Murlet(20): 0.593 Positive Predictive Value TurboFold(20): 0.817 Murlet(20): 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.773 PknotsRG: 0.696 Sensitivity TurboFold(20): 0.737 PknotsRG: 0.718 Positive Predictive Value TurboFold(20): 0.817 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.773 RNAfold: 0.674 Sensitivity TurboFold(20): 0.737 RNAfold: 0.686 Positive Predictive Value TurboFold(20): 0.817 RNAfold: 0.671 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.773 RNAshapes: 0.669 Sensitivity TurboFold(20): 0.737 RNAshapes: 0.678 Positive Predictive Value TurboFold(20): 0.817 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.773 Fold: 0.634 Sensitivity TurboFold(20): 0.737 Fold: 0.656 Positive Predictive Value TurboFold(20): 0.817 Fold: 0.622 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.694 TurboFold(seed): 0.683 Sensitivity TurboFold(20): 0.653 TurboFold(seed): 0.653 Positive Predictive Value TurboFold(20): 0.746 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.740 Afold: 0.713 Sensitivity TurboFold(20): 0.705 Afold: 0.723 Positive Predictive Value TurboFold(20): 0.782 Afold: 0.711 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): 0.773 Carnac(20): 0.638 Sensitivity TurboFold(20): 0.737 Carnac(20): 0.491 Positive Predictive Value TurboFold(20): 0.817 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.758 RSpredict(20): 0.624 Sensitivity TurboFold(20): 0.748 RSpredict(20): 0.572 Positive Predictive Value TurboFold(20): 0.773 RSpredict(20): 0.689 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.773 RNAsubopt: 0.672 Sensitivity TurboFold(20): 0.737 RNAsubopt: 0.688 Positive Predictive Value TurboFold(20): 0.817 RNAsubopt: 0.665 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.836 Cylofold: 0.768 Sensitivity TurboFold(20): 0.788 Cylofold: 0.753 Positive Predictive Value TurboFold(20): 0.892 Cylofold: 0.792 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.773 McQFold: 0.680 Sensitivity TurboFold(20): 0.737 McQFold: 0.678 Positive Predictive Value TurboFold(20): 0.817 McQFold: 0.691 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.755 RNASLOpt: 0.635 Sensitivity TurboFold(20): 0.717 RNASLOpt: 0.616 Positive Predictive Value TurboFold(20): 0.800 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	+ TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.773 Pknots: 0.591 Sensitivity TurboFold(20): 0.737 Pknots: 0.621 Positive Predictive Value TurboFold(20): 0.817 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.683 CRWrnafold: 0.668 Sensitivity TurboFold(20): 0.646 CRWrnafold: 0.683 Positive Predictive Value TurboFold(20): 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.796 Multilign(20): 0.699 Sensitivity TurboFold(20): 0.762 Multilign(20): 0.688 Positive Predictive Value TurboFold(20): 0.838 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	? TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.641 RNASampler(seed): 0.617 Sensitivity TurboFold(20): 0.625 RNASampler(seed): 0.525 Positive Predictive Value TurboFold(20): 0.664 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.829 Alterna: 0.750 Sensitivity TurboFold(20): 0.800 Alterna: 0.756 Positive Predictive Value TurboFold(20): 0.867 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.773 Mastr(20): 0.631 Sensitivity TurboFold(20): 0.737 Mastr(20): 0.509 Positive Predictive Value TurboFold(20): 0.817 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.14531876181e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.796 Vsfold4: 0.619 Sensitivity TurboFold(20): 0.762 Vsfold4: 0.603 Positive Predictive Value TurboFold(20): 0.838 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.45096400029e-08	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.691 Murlet(seed): 0.543 Sensitivity TurboFold(20): 0.645 Murlet(seed): 0.360 Positive Predictive Value TurboFold(20): 0.749 Murlet(seed): 0.830 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.752 MCFold: 0.518 Sensitivity TurboFold(20): 0.747 MCFold: 0.574 Positive Predictive Value TurboFold(20): 0.762 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.796 Vsfold5: 0.546 Sensitivity TurboFold(20): 0.762 Vsfold5: 0.544 Positive Predictive Value TurboFold(20): 0.838 Vsfold5: 0.561 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.751 RNAwolf: 0.429 Sensitivity TurboFold(20): 0.741 RNAwolf: 0.446 Positive Predictive Value TurboFold(20): 0.766 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.872 CMfinder(20): 0.652 Sensitivity TurboFold(20): 0.842 CMfinder(20): 0.518 Positive Predictive Value TurboFold(20): 0.906 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.773 NanoFolder: 0.329 Sensitivity TurboFold(20): 0.742 NanoFolder: 0.405 Positive Predictive Value TurboFold(20): 0.810 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.776 RDfolder: 0.584 Sensitivity TurboFold(20): 0.724 RDfolder: 0.518 Positive Predictive Value TurboFold(20): 0.842 RDfolder: 0.677 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): 0.758 RSpredict(seed): 0.180 Sensitivity TurboFold(20): 0.748 RSpredict(seed): 0.086 Positive Predictive Value TurboFold(20): 0.773 RSpredict(seed): 0.394 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 TurboFold(20): 0.724 Sensitivity Multilign(seed): 0.682 TurboFold(20): 0.674 Positive Predictive Value Multilign(seed): 0.793 TurboFold(20): 0.784 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.764 PPfold(seed): 0.046 Sensitivity TurboFold(20): 0.726 PPfold(seed): 0.009 Positive Predictive Value TurboFold(20): 0.810 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.718 Carnac(seed): 0.272 Sensitivity TurboFold(20): 0.675 Carnac(seed): 0.075 Positive Predictive Value TurboFold(20): 0.771 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.773 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.737 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.817 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidAlifold(seed)	39 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 CentroidAlifold(seed): 0.695 Sensitivity CentroidAlifold(20): 0.728 CentroidAlifold(seed): 0.528 Positive Predictive Value CentroidAlifold(20): 0.901 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 CentroidAlifold(seed): 0.762 Sensitivity PETfold_pre2.0(seed): 0.841 CentroidAlifold(seed): 0.625 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	26 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.805 CentroidAlifold(seed): 0.762 Sensitivity ContextFold: 0.784 CentroidAlifold(seed): 0.625 Positive Predictive Value ContextFold: 0.827 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	60 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.780 CentroidAlifold(seed): 0.735 Sensitivity MXScarna(seed): 0.744 CentroidAlifold(seed): 0.605 Positive Predictive Value MXScarna(seed): 0.819 CentroidAlifold(seed): 0.894 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.783 CentroidAlifold(seed): 0.695 Sensitivity RNAalifold(20): 0.710 CentroidAlifold(seed): 0.528 Positive Predictive Value RNAalifold(20): 0.867 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 CentroidAlifold(seed): 0.650 Sensitivity PETfold_pre2.0(20): 0.776 CentroidAlifold(seed): 0.449 Positive Predictive Value PETfold_pre2.0(20): 0.815 CentroidAlifold(seed): 0.947 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48104284388e-08	21 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.793 CentroidAlifold(seed): 0.667 Sensitivity PPfold(20): 0.752 CentroidAlifold(seed): 0.480 Positive Predictive Value PPfold(20): 0.841 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.764 IPknot: 0.717 Sensitivity CentroidAlifold(seed): 0.627 IPknot: 0.704 Positive Predictive Value CentroidAlifold(seed): 0.932 IPknot: 0.731 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.57333037898e-08	39 MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 CentroidAlifold(seed): 0.695 Sensitivity MXScarna(20): 0.724 CentroidAlifold(seed): 0.528 Positive Predictive Value MXScarna(20): 0.780 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.738 CentroidAlifold(seed): 0.695 Sensitivity RNASampler(20): 0.667 CentroidAlifold(seed): 0.528 Positive Predictive Value RNASampler(20): 0.822 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.758 CentroidAlifold(seed): 0.667 Sensitivity TurboFold(20): 0.748 CentroidAlifold(seed): 0.480 Positive Predictive Value TurboFold(20): 0.773 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08		+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CentroidFold: 0.718 Sensitivity CentroidAlifold(seed): 0.602 CentroidFold: 0.718 Positive Predictive Value CentroidAlifold(seed): 0.894 CentroidFold: 0.720 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 6.70530687003e-06	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Sfold: 0.669 Sensitivity CentroidAlifold(seed): 0.602 Sfold: 0.665 Positive Predictive Value CentroidAlifold(seed): 0.894 Sfold: 0.674 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.1569883686e-08	- CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 CentroidAlifold(seed): 0.670 Sensitivity CentroidHomfold‑LAST: 0.708 CentroidAlifold(seed): 0.486 Positive Predictive Value CentroidHomfold‑LAST: 0.727 CentroidAlifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Contrafold: 0.699 Sensitivity CentroidAlifold(seed): 0.602 Contrafold: 0.722 Positive Predictive Value CentroidAlifold(seed): 0.894 Contrafold: 0.678 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 RNAalifold(seed): 0.734 Sensitivity CentroidAlifold(seed): 0.702 RNAalifold(seed): 0.612 Positive Predictive Value CentroidAlifold(seed): 0.881 RNAalifold(seed): 0.882 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.735 MaxExpect: 0.672 Sensitivity CentroidAlifold(seed): 0.606 MaxExpect: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.892 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 HotKnots: 0.671 Sensitivity CentroidAlifold(seed): 0.535 HotKnots: 0.706 Positive Predictive Value CentroidAlifold(seed): 0.884 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 4.57295429596e-06	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 UNAFold: 0.649 Sensitivity CentroidAlifold(seed): 0.602 UNAFold: 0.670 Positive Predictive Value CentroidAlifold(seed): 0.894 UNAFold: 0.631 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 ProbKnot: 0.647 Sensitivity CentroidAlifold(seed): 0.610 ProbKnot: 0.673 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.624 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Murlet(20): 0.702 CentroidAlifold(seed): 0.695 Sensitivity Murlet(20): 0.610 CentroidAlifold(seed): 0.528 Positive Predictive Value Murlet(20): 0.814 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.0144324399527	= PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.690 CentroidAlifold(seed): 0.686 Sensitivity PknotsRG: 0.722 CentroidAlifold(seed): 0.535 Positive Predictive Value PknotsRG: 0.665 CentroidAlifold(seed): 0.884 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 0.211284698433	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RNAfold: 0.658 Sensitivity CentroidAlifold(seed): 0.602 RNAfold: 0.682 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAfold: 0.638 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNAshapes: 0.669 Sensitivity CentroidAlifold(seed): 0.535 RNAshapes: 0.693 Positive Predictive Value CentroidAlifold(seed): 0.884 RNAshapes: 0.653 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 6.58294707158e-07	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.736 Fold: 0.659 Sensitivity CentroidAlifold(seed): 0.608 Fold: 0.688 Positive Predictive Value CentroidAlifold(seed): 0.893 Fold: 0.633 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 8.81311508309e-08	+ CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 TurboFold(seed): 0.653 Sensitivity CentroidAlifold(seed): 0.558 TurboFold(seed): 0.641 Positive Predictive Value CentroidAlifold(seed): 0.916 TurboFold(seed): 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.671 Afold: 0.646 Sensitivity CentroidAlifold(seed): 0.536 Afold: 0.681 Positive Predictive Value CentroidAlifold(seed): 0.845 Afold: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08	= Carnac(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Carnac(20): 0.695 CentroidAlifold(seed): 0.695 Sensitivity Carnac(20): 0.529 CentroidAlifold(seed): 0.528 Positive Predictive Value Carnac(20): 0.918 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.88245777838	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 RSpredict(20): 0.657 Sensitivity CentroidAlifold(seed): 0.530 RSpredict(20): 0.595 Positive Predictive Value CentroidAlifold(seed): 0.923 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNAsubopt: 0.668 Sensitivity CentroidAlifold(seed): 0.535 RNAsubopt: 0.701 Positive Predictive Value CentroidAlifold(seed): 0.884 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 2.63254822069e-07	+ CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 Cylofold: 0.704 Sensitivity CentroidAlifold(seed): 0.554 Cylofold: 0.694 Positive Predictive Value CentroidAlifold(seed): 0.941 Cylofold: 0.723 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.33397498022e-05	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 McQFold: 0.623 Sensitivity CentroidAlifold(seed): 0.602 McQFold: 0.633 Positive Predictive Value CentroidAlifold(seed): 0.894 McQFold: 0.615 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.666 RNASLOpt: 0.591 Sensitivity CentroidAlifold(seed): 0.475 RNASLOpt: 0.579 Positive Predictive Value CentroidAlifold(seed): 0.941 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.700 Pknots: 0.664 Sensitivity CentroidAlifold(seed): 0.542 Pknots: 0.700 Positive Predictive Value CentroidAlifold(seed): 0.911 Pknots: 0.639 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.85233844192e-08	? CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.678 CRWrnafold: 0.647 Sensitivity CentroidAlifold(seed): 0.473 CRWrnafold: 0.655 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.685 Multilign(20): 0.625 Sensitivity CentroidAlifold(seed): 0.506 Multilign(20): 0.611 Positive Predictive Value CentroidAlifold(seed): 0.934 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNASampler(seed): 0.681 Sensitivity CentroidAlifold(seed): 0.631 RNASampler(seed): 0.593 Positive Predictive Value CentroidAlifold(seed): 0.852 RNASampler(seed): 0.789 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.753 CentroidAlifold(seed): 0.673 Sensitivity Alterna: 0.761 CentroidAlifold(seed): 0.531 Positive Predictive Value Alterna: 0.756 CentroidAlifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 Mastr(20): 0.610 Sensitivity CentroidAlifold(seed): 0.528 Mastr(20): 0.475 Positive Predictive Value CentroidAlifold(seed): 0.921 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.681 Vsfold4: 0.582 Sensitivity CentroidAlifold(seed): 0.529 Vsfold4: 0.582 Positive Predictive Value CentroidAlifold(seed): 0.882 Vsfold4: 0.590 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 Murlet(seed): 0.584 Sensitivity CentroidAlifold(seed): 0.682 Murlet(seed): 0.402 Positive Predictive Value CentroidAlifold(seed): 0.891 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 MCFold: 0.553 Sensitivity CentroidAlifold(seed): 0.538 MCFold: 0.605 Positive Predictive Value CentroidAlifold(seed): 0.905 MCFold: 0.518 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 Vsfold5: 0.548 Sensitivity CentroidAlifold(seed): 0.533 Vsfold5: 0.556 Positive Predictive Value CentroidAlifold(seed): 0.883 Vsfold5: 0.549 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.764 RNAwolf: 0.509 Sensitivity CentroidAlifold(seed): 0.627 RNAwolf: 0.510 Positive Predictive Value CentroidAlifold(seed): 0.932 RNAwolf: 0.511 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	- CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.648 CentroidAlifold(seed): 0.630 Sensitivity CMfinder(20): 0.563 CentroidAlifold(seed): 0.430 Positive Predictive Value CMfinder(20): 0.754 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.48061257066e-07	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.643 NanoFolder: 0.340 Sensitivity CentroidAlifold(seed): 0.441 NanoFolder: 0.430 Positive Predictive Value CentroidAlifold(seed): 0.944 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.688 RDfolder: 0.624 Sensitivity CentroidAlifold(seed): 0.543 RDfolder: 0.592 Positive Predictive Value CentroidAlifold(seed): 0.883 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.735 RSpredict(seed): 0.446 Sensitivity CentroidAlifold(seed): 0.604 RSpredict(seed): 0.302 Positive Predictive Value CentroidAlifold(seed): 0.895 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 Multilign(seed): 0.679 Sensitivity CentroidAlifold(seed): 0.612 Multilign(seed): 0.629 Positive Predictive Value CentroidAlifold(seed): 0.909 Multilign(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.76606667793e-09	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 PPfold(seed): 0.157 Sensitivity CentroidAlifold(seed): 0.496 PPfold(seed): 0.040 Positive Predictive Value CentroidAlifold(seed): 0.950 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.804 Carnac(seed): 0.467 Sensitivity CentroidAlifold(seed): 0.715 Carnac(seed): 0.232 Positive Predictive Value CentroidAlifold(seed): 0.905 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 Mastr(seed): 0.261 Sensitivity CentroidAlifold(seed): 0.535 Mastr(seed): 0.079 Positive Predictive Value CentroidAlifold(seed): 0.884 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 CentroidAlifold(seed): 0.756 Sensitivity PETfold_2.0(seed): 0.845 CentroidAlifold(seed): 0.638 Positive Predictive Value PETfold_2.0(seed): 0.891 CentroidAlifold(seed): 0.902 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidAlifold(seed): 0.615 Sensitivity PETfold_2.0(20): 0.889 CentroidAlifold(seed): 0.444 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidAlifold(seed): 0.857 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidFold	39 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 CentroidFold: 0.690 Sensitivity CentroidAlifold(20): 0.728 CentroidFold: 0.689 Positive Predictive Value CentroidAlifold(20): 0.901 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 CentroidFold: 0.698 Sensitivity PETfold_pre2.0(seed): 0.841 CentroidFold: 0.689 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidFold: 0.707 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	61 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.683 CentroidFold: 0.614 Sensitivity ContextFold: 0.677 CentroidFold: 0.600 Positive Predictive Value ContextFold: 0.691 CentroidFold: 0.631 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.780 CentroidFold: 0.718 Sensitivity MXScarna(seed): 0.744 CentroidFold: 0.718 Positive Predictive Value MXScarna(seed): 0.819 CentroidFold: 0.721 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.783 CentroidFold: 0.690 Sensitivity RNAalifold(20): 0.710 CentroidFold: 0.689 Positive Predictive Value RNAalifold(20): 0.867 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 CentroidFold: 0.644 Sensitivity PETfold_pre2.0(20): 0.776 CentroidFold: 0.652 Positive Predictive Value PETfold_pre2.0(20): 0.815 CentroidFold: 0.643 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	21 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.793 CentroidFold: 0.671 Sensitivity PPfold(20): 0.752 CentroidFold: 0.674 Positive Predictive Value PPfold(20): 0.841 CentroidFold: 0.675 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	69 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.669 CentroidFold: 0.627 Sensitivity IPknot: 0.645 CentroidFold: 0.613 Positive Predictive Value IPknot: 0.695 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.749 CentroidFold: 0.690 Sensitivity MXScarna(20): 0.724 CentroidFold: 0.689 Positive Predictive Value MXScarna(20): 0.780 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.738 CentroidFold: 0.690 Sensitivity RNASampler(20): 0.667 CentroidFold: 0.689 Positive Predictive Value RNASampler(20): 0.822 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.758 CentroidFold: 0.671 Sensitivity TurboFold(20): 0.748 CentroidFold: 0.674 Positive Predictive Value TurboFold(20): 0.773 CentroidFold: 0.675 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	61 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CentroidFold: 0.718 Sensitivity CentroidAlifold(seed): 0.602 CentroidFold: 0.718 Positive Predictive Value CentroidAlifold(seed): 0.894 CentroidFold: 0.720 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 6.70530687003e-06		+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.667 Sfold: 0.627 Sensitivity CentroidFold: 0.661 Sfold: 0.630 Positive Predictive Value CentroidFold: 0.675 Sfold: 0.624 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 CentroidFold: 0.702 Sensitivity CentroidHomfold‑LAST: 0.637 CentroidFold: 0.698 Positive Predictive Value CentroidHomfold‑LAST: 0.781 CentroidFold: 0.712 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 0.978553375983	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.667 Contrafold: 0.649 Sensitivity CentroidFold: 0.661 Contrafold: 0.675 Positive Predictive Value CentroidFold: 0.675 Contrafold: 0.625 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.734 CentroidFold: 0.708 Sensitivity RNAalifold(seed): 0.612 CentroidFold: 0.702 Positive Predictive Value RNAalifold(seed): 0.882 CentroidFold: 0.715 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.000218715568349	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.693 MaxExpect: 0.660 Sensitivity CentroidFold: 0.679 MaxExpect: 0.677 Positive Predictive Value CentroidFold: 0.708 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.737 HotKnots: 0.722 Sensitivity CentroidFold: 0.736 HotKnots: 0.752 Positive Predictive Value CentroidFold: 0.743 HotKnots: 0.700 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.667 UNAFold: 0.600 Sensitivity CentroidFold: 0.661 UNAFold: 0.634 Positive Predictive Value CentroidFold: 0.675 UNAFold: 0.568 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.668 ProbKnot: 0.635 Sensitivity CentroidFold: 0.659 ProbKnot: 0.665 Positive Predictive Value CentroidFold: 0.679 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.702 CentroidFold: 0.690 Sensitivity Murlet(20): 0.610 CentroidFold: 0.689 Positive Predictive Value Murlet(20): 0.814 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 2.12176083234e-07	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.664 PknotsRG: 0.592 Sensitivity CentroidFold: 0.658 PknotsRG: 0.635 Positive Predictive Value CentroidFold: 0.672 PknotsRG: 0.552 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.667 RNAfold: 0.593 Sensitivity CentroidFold: 0.661 RNAfold: 0.633 Positive Predictive Value CentroidFold: 0.675 RNAfold: 0.557 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.737 RNAshapes: 0.697 Sensitivity CentroidFold: 0.736 RNAshapes: 0.717 Positive Predictive Value CentroidFold: 0.743 RNAshapes: 0.683 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.683 Fold: 0.633 Sensitivity CentroidFold: 0.673 Fold: 0.666 Positive Predictive Value CentroidFold: 0.694 Fold: 0.604 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.665 TurboFold(seed): 0.653 Sensitivity CentroidFold: 0.638 TurboFold(seed): 0.641 Positive Predictive Value CentroidFold: 0.700 TurboFold(seed): 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.48358879813e-06	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.649 Afold: 0.563 Sensitivity CentroidFold: 0.643 Afold: 0.610 Positive Predictive Value CentroidFold: 0.656 Afold: 0.520 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.695 CentroidFold: 0.690 Sensitivity Carnac(20): 0.529 CentroidFold: 0.689 Positive Predictive Value Carnac(20): 0.918 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.8192559593	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.689 RSpredict(20): 0.657 Sensitivity CentroidFold: 0.687 RSpredict(20): 0.595 Positive Predictive Value CentroidFold: 0.697 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.737 RNAsubopt: 0.698 Sensitivity CentroidFold: 0.736 RNAsubopt: 0.730 Positive Predictive Value CentroidFold: 0.743 RNAsubopt: 0.674 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.783 Cylofold: 0.699 Sensitivity CentroidFold: 0.771 Cylofold: 0.686 Positive Predictive Value CentroidFold: 0.802 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.666 McQFold: 0.521 Sensitivity CentroidFold: 0.660 McQFold: 0.502 Positive Predictive Value CentroidFold: 0.674 McQFold: 0.543 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.673 RNASLOpt: 0.582 Sensitivity CentroidFold: 0.670 RNASLOpt: 0.568 Positive Predictive Value CentroidFold: 0.683 RNASLOpt: 0.605 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.772 Pknots: 0.689 Sensitivity CentroidFold: 0.764 Pknots: 0.718 Positive Predictive Value CentroidFold: 0.787 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.737 CRWrnafold: 0.683 Sensitivity CentroidFold: 0.717 CRWrnafold: 0.690 Positive Predictive Value CentroidFold: 0.767 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.648 Multilign(20): 0.625 Sensitivity CentroidFold: 0.654 Multilign(20): 0.611 Positive Predictive Value CentroidFold: 0.652 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.88012384877e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.757 RNASampler(seed): 0.681 Sensitivity CentroidFold: 0.749 RNASampler(seed): 0.593 Positive Predictive Value CentroidFold: 0.770 RNASampler(seed): 0.789 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.848 Alterna: 0.750 Sensitivity CentroidFold: 0.827 Alterna: 0.762 Positive Predictive Value CentroidFold: 0.877 Alterna: 0.750 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.690 Mastr(20): 0.610 Sensitivity CentroidFold: 0.689 Mastr(20): 0.475 Positive Predictive Value CentroidFold: 0.698 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.747 Vsfold4: 0.610 Sensitivity CentroidFold: 0.747 Vsfold4: 0.601 Positive Predictive Value CentroidFold: 0.753 Vsfold4: 0.628 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.758 Murlet(seed): 0.584 Sensitivity CentroidFold: 0.736 Murlet(seed): 0.402 Positive Predictive Value CentroidFold: 0.788 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.765 MCFold: 0.608 Sensitivity CentroidFold: 0.759 MCFold: 0.649 Positive Predictive Value CentroidFold: 0.779 MCFold: 0.582 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.752 Vsfold5: 0.572 Sensitivity CentroidFold: 0.751 Vsfold5: 0.576 Positive Predictive Value CentroidFold: 0.758 Vsfold5: 0.578 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.627 RNAwolf: 0.436 Sensitivity CentroidFold: 0.613 RNAwolf: 0.446 Positive Predictive Value CentroidFold: 0.644 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.648 CentroidFold: 0.645 Sensitivity CMfinder(20): 0.563 CentroidFold: 0.680 Positive Predictive Value CMfinder(20): 0.754 CentroidFold: 0.619 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00868291460752	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.667 NanoFolder: 0.395 Sensitivity CentroidFold: 0.673 NanoFolder: 0.495 Positive Predictive Value CentroidFold: 0.668 NanoFolder: 0.329 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.830 RDfolder: 0.659 Sensitivity CentroidFold: 0.810 RDfolder: 0.618 Positive Predictive Value CentroidFold: 0.858 RDfolder: 0.719 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.718 RSpredict(seed): 0.446 Sensitivity CentroidFold: 0.718 RSpredict(seed): 0.302 Positive Predictive Value CentroidFold: 0.720 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.736 Multilign(seed): 0.679 Sensitivity CentroidFold: 0.680 Multilign(seed): 0.629 Positive Predictive Value CentroidFold: 0.804 Multilign(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.703 PPfold(seed): 0.157 Sensitivity CentroidFold: 0.692 PPfold(seed): 0.040 Positive Predictive Value CentroidFold: 0.722 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.743 Carnac(seed): 0.467 Sensitivity CentroidFold: 0.730 Carnac(seed): 0.232 Positive Predictive Value CentroidFold: 0.758 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.722 Mastr(seed): 0.261 Sensitivity CentroidFold: 0.725 Mastr(seed): 0.079 Positive Predictive Value CentroidFold: 0.724 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 CentroidFold: 0.853 Sensitivity PETfold_2.0(seed): 0.845 CentroidFold: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 CentroidFold: 0.847 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidFold: 0.725 Sensitivity PETfold_2.0(20): 0.889 CentroidFold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidFold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Sfold	39 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Sfold: 0.680 Sensitivity CentroidAlifold(20): 0.728 Sfold: 0.667 Positive Predictive Value CentroidAlifold(20): 0.901 Sfold: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Sfold: 0.612 Sensitivity PETfold_pre2.0(seed): 0.841 Sfold: 0.608 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Sfold: 0.619 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	49 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.680 Sfold: 0.592 Sensitivity ContextFold: 0.671 Sfold: 0.596 Positive Predictive Value ContextFold: 0.689 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.786 Sfold: 0.671 Sensitivity MXScarna(seed): 0.749 Sfold: 0.665 Positive Predictive Value MXScarna(seed): 0.825 Sfold: 0.680 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.790 Sfold: 0.707 Sensitivity RNAalifold(20): 0.704 Sfold: 0.683 Positive Predictive Value RNAalifold(20): 0.891 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Sfold: 0.623 Sensitivity PETfold_pre2.0(20): 0.776 Sfold: 0.622 Positive Predictive Value PETfold_pre2.0(20): 0.815 Sfold: 0.631 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	15 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.812 Sfold: 0.703 Sensitivity PPfold(20): 0.753 Sfold: 0.675 Positive Predictive Value PPfold(20): 0.880 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.18011954625e-08	57 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.675 Sfold: 0.604 Sensitivity IPknot: 0.645 Sfold: 0.607 Positive Predictive Value IPknot: 0.707 Sfold: 0.603 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.755 Sfold: 0.707 Sensitivity MXScarna(20): 0.720 Sfold: 0.683 Positive Predictive Value MXScarna(20): 0.796 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.751 Sfold: 0.707 Sensitivity RNASampler(20): 0.663 Sfold: 0.683 Positive Predictive Value RNASampler(20): 0.856 Sfold: 0.736 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.773 Sfold: 0.703 Sensitivity TurboFold(20): 0.737 Sfold: 0.675 Positive Predictive Value TurboFold(20): 0.817 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.00627773251e-08	61 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Sfold: 0.669 Sensitivity CentroidAlifold(seed): 0.602 Sfold: 0.665 Positive Predictive Value CentroidAlifold(seed): 0.894 Sfold: 0.674 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.1569883686e-08	137 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.667 Sfold: 0.627 Sensitivity CentroidFold: 0.661 Sfold: 0.630 Positive Predictive Value CentroidFold: 0.675 Sfold: 0.624 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.732 CentroidHomfold‑LAST: 0.708 Sensitivity Sfold: 0.719 CentroidHomfold‑LAST: 0.629 Positive Predictive Value Sfold: 0.751 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 4.83792096436e-08	- Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.662 Sfold: 0.613 Sensitivity Contrafold: 0.684 Sfold: 0.614 Positive Predictive Value Contrafold: 0.640 Sfold: 0.612 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.740 Sfold: 0.659 Sensitivity RNAalifold(seed): 0.624 Sfold: 0.653 Positive Predictive Value RNAalifold(seed): 0.879 Sfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.10039559051e-07	- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.663 Sfold: 0.649 Sensitivity MaxExpect: 0.679 Sfold: 0.645 Positive Predictive Value MaxExpect: 0.648 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.000243049897693	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.755 HotKnots: 0.737 Sensitivity Sfold: 0.746 HotKnots: 0.761 Positive Predictive Value Sfold: 0.769 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.613 UNAFold: 0.589 Sensitivity Sfold: 0.614 UNAFold: 0.620 Positive Predictive Value Sfold: 0.612 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.659 ProbKnot: 0.638 Sensitivity Sfold: 0.663 ProbKnot: 0.668 Positive Predictive Value Sfold: 0.656 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.707 Murlet(20): 0.693 Sensitivity Sfold: 0.683 Murlet(20): 0.594 Positive Predictive Value Sfold: 0.736 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.37177523642e-07	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.616 PknotsRG: 0.575 Sensitivity Sfold: 0.617 PknotsRG: 0.613 Positive Predictive Value Sfold: 0.616 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.613 RNAfold: 0.583 Sensitivity Sfold: 0.614 RNAfold: 0.619 Positive Predictive Value Sfold: 0.612 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.755 RNAshapes: 0.714 Sensitivity Sfold: 0.746 RNAshapes: 0.731 Positive Predictive Value Sfold: 0.769 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.671 Fold: 0.636 Sensitivity Sfold: 0.674 Fold: 0.668 Positive Predictive Value Sfold: 0.670 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.666 TurboFold(seed): 0.647 Sensitivity Sfold: 0.611 TurboFold(seed): 0.615 Positive Predictive Value Sfold: 0.734 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.40944795717e-06	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.591 Afold: 0.564 Sensitivity Sfold: 0.595 Afold: 0.605 Positive Predictive Value Sfold: 0.587 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.707 Carnac(20): 0.686 Sensitivity Sfold: 0.683 Carnac(20): 0.518 Positive Predictive Value Sfold: 0.736 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.682 RSpredict(20): 0.660 Sensitivity Sfold: 0.669 RSpredict(20): 0.597 Positive Predictive Value Sfold: 0.700 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.755 RNAsubopt: 0.703 Sensitivity Sfold: 0.746 RNAsubopt: 0.730 Positive Predictive Value Sfold: 0.769 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.760 Cylofold: 0.701 Sensitivity Sfold: 0.744 Cylofold: 0.686 Positive Predictive Value Sfold: 0.784 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.612 McQFold: 0.501 Sensitivity Sfold: 0.613 McQFold: 0.483 Positive Predictive Value Sfold: 0.611 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.690 RNASLOpt: 0.580 Sensitivity Sfold: 0.676 RNASLOpt: 0.559 Positive Predictive Value Sfold: 0.710 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.790 Pknots: 0.705 Sensitivity Sfold: 0.773 Pknots: 0.732 Positive Predictive Value Sfold: 0.814 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.711 CRWrnafold: 0.683 Sensitivity Sfold: 0.692 CRWrnafold: 0.690 Positive Predictive Value Sfold: 0.741 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.693 Multilign(20): 0.652 Sensitivity Sfold: 0.669 Multilign(20): 0.624 Positive Predictive Value Sfold: 0.728 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.785 RNASampler(seed): 0.728 Sensitivity Sfold: 0.771 RNASampler(seed): 0.634 Positive Predictive Value Sfold: 0.805 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.827 Alterna: 0.767 Sensitivity Sfold: 0.809 Alterna: 0.777 Positive Predictive Value Sfold: 0.854 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.707 Mastr(20): 0.620 Sensitivity Sfold: 0.683 Mastr(20): 0.473 Positive Predictive Value Sfold: 0.736 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.761 Vsfold4: 0.635 Sensitivity Sfold: 0.753 Vsfold4: 0.625 Positive Predictive Value Sfold: 0.775 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.759 Murlet(seed): 0.594 Sensitivity Sfold: 0.723 Murlet(seed): 0.418 Positive Predictive Value Sfold: 0.803 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.781 MCFold: 0.622 Sensitivity Sfold: 0.770 MCFold: 0.663 Positive Predictive Value Sfold: 0.799 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.754 Vsfold5: 0.593 Sensitivity Sfold: 0.745 Vsfold5: 0.595 Positive Predictive Value Sfold: 0.770 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.611 RNAwolf: 0.436 Sensitivity Sfold: 0.614 RNAwolf: 0.446 Positive Predictive Value Sfold: 0.608 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.729 CMfinder(20): 0.652 Sensitivity Sfold: 0.719 CMfinder(20): 0.518 Positive Predictive Value Sfold: 0.745 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.681 NanoFolder: 0.394 Sensitivity Sfold: 0.679 NanoFolder: 0.485 Positive Predictive Value Sfold: 0.692 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.812 RDfolder: 0.677 Sensitivity Sfold: 0.793 RDfolder: 0.637 Positive Predictive Value Sfold: 0.841 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.670 RSpredict(seed): 0.449 Sensitivity Sfold: 0.667 RSpredict(seed): 0.304 Positive Predictive Value Sfold: 0.675 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.681 Multilign(seed): 0.649 Sensitivity Sfold: 0.625 Multilign(seed): 0.591 Positive Predictive Value Sfold: 0.751 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.658 PPfold(seed): 0.094 Sensitivity Sfold: 0.621 PPfold(seed): 0.019 Positive Predictive Value Sfold: 0.706 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.704 Carnac(seed): 0.474 Sensitivity Sfold: 0.690 Carnac(seed): 0.239 Positive Predictive Value Sfold: 0.719 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.705 Mastr(seed): 0.279 Sensitivity Sfold: 0.693 Mastr(seed): 0.088 Positive Predictive Value Sfold: 0.723 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Sfold: 0.858 Sensitivity PETfold_2.0(seed): 0.845 Sfold: 0.845 Positive Predictive Value PETfold_2.0(seed): 0.891 Sfold: 0.875 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Sfold: 0.729 Sensitivity PETfold_2.0(20): 0.889 Sfold: 0.704 Positive Predictive Value PETfold_2.0(20): 0.923 Sfold: 0.760 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CentroidHomfold‑LAST	21 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.822 CentroidHomfold‑LAST: 0.725 Sensitivity CentroidAlifold(20): 0.763 CentroidHomfold‑LAST: 0.723 Positive Predictive Value CentroidAlifold(20): 0.890 CentroidHomfold‑LAST: 0.733 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.876 CentroidHomfold‑LAST: 0.691 Sensitivity PETfold_pre2.0(seed): 0.839 CentroidHomfold‑LAST: 0.693 Positive Predictive Value PETfold_pre2.0(seed): 0.916 CentroidHomfold‑LAST: 0.696 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.787 CentroidHomfold‑LAST: 0.677 Sensitivity ContextFold: 0.765 CentroidHomfold‑LAST: 0.601 Positive Predictive Value ContextFold: 0.812 CentroidHomfold‑LAST: 0.767 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.743 CentroidHomfold‑LAST: 0.728 Sensitivity MXScarna(seed): 0.700 CentroidHomfold‑LAST: 0.715 Positive Predictive Value MXScarna(seed): 0.798 CentroidHomfold‑LAST: 0.749 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.66134940242e-07	14 RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.796 CentroidHomfold‑LAST: 0.760 Sensitivity RNAalifold(20): 0.735 CentroidHomfold‑LAST: 0.744 Positive Predictive Value RNAalifold(20): 0.868 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.85493025655e-08	17 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 CentroidHomfold‑LAST: 0.697 Sensitivity PETfold_pre2.0(20): 0.814 CentroidHomfold‑LAST: 0.706 Positive Predictive Value PETfold_pre2.0(20): 0.847 CentroidHomfold‑LAST: 0.694 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	14 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.844 CentroidHomfold‑LAST: 0.760 Sensitivity PPfold(20): 0.791 CentroidHomfold‑LAST: 0.744 Positive Predictive Value PPfold(20): 0.906 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	49 IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.760 CentroidHomfold‑LAST: 0.704 Sensitivity IPknot: 0.747 CentroidHomfold‑LAST: 0.628 Positive Predictive Value IPknot: 0.777 CentroidHomfold‑LAST: 0.794 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 MXScarna(20): 0.737 Sensitivity CentroidHomfold‑LAST: 0.744 MXScarna(20): 0.700 Positive Predictive Value CentroidHomfold‑LAST: 0.783 MXScarna(20): 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.97503173922e-08	14 RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.774 CentroidHomfold‑LAST: 0.760 Sensitivity RNASampler(20): 0.700 CentroidHomfold‑LAST: 0.744 Positive Predictive Value RNASampler(20): 0.862 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.33374751016e-06	14 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.796 CentroidHomfold‑LAST: 0.760 Sensitivity TurboFold(20): 0.762 CentroidHomfold‑LAST: 0.744 Positive Predictive Value TurboFold(20): 0.838 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.36290909588e-08	27 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 CentroidAlifold(seed): 0.670 Sensitivity CentroidHomfold‑LAST: 0.708 CentroidAlifold(seed): 0.486 Positive Predictive Value CentroidHomfold‑LAST: 0.727 CentroidAlifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	67 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 CentroidFold: 0.702 Sensitivity CentroidHomfold‑LAST: 0.637 CentroidFold: 0.698 Positive Predictive Value CentroidHomfold‑LAST: 0.781 CentroidFold: 0.712 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 0.978553375983	56 Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.732 CentroidHomfold‑LAST: 0.708 Sensitivity Sfold: 0.719 CentroidHomfold‑LAST: 0.629 Positive Predictive Value Sfold: 0.751 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 4.83792096436e-08		- Contrafold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Contrafold: 0.714 CentroidHomfold‑LAST: 0.708 Sensitivity Contrafold: 0.728 CentroidHomfold‑LAST: 0.629 Positive Predictive Value Contrafold: 0.706 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.000218715568349	- RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.664 CentroidHomfold‑LAST: 0.638 Sensitivity RNAalifold(seed): 0.518 CentroidHomfold‑LAST: 0.617 Positive Predictive Value RNAalifold(seed): 0.862 CentroidHomfold‑LAST: 0.672 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.81480685939e-07	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 MaxExpect: 0.669 Sensitivity CentroidHomfold‑LAST: 0.629 MaxExpect: 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.803 MaxExpect: 0.665 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.721 CentroidHomfold‑LAST: 0.708 Sensitivity HotKnots: 0.735 CentroidHomfold‑LAST: 0.629 Positive Predictive Value HotKnots: 0.712 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.53079410487e-06	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 UNAFold: 0.688 Sensitivity CentroidHomfold‑LAST: 0.629 UNAFold: 0.700 Positive Predictive Value CentroidHomfold‑LAST: 0.803 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 ProbKnot: 0.668 Sensitivity CentroidHomfold‑LAST: 0.629 ProbKnot: 0.695 Positive Predictive Value CentroidHomfold‑LAST: 0.803 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Murlet(20): 0.684 Sensitivity CentroidHomfold‑LAST: 0.744 Murlet(20): 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 PknotsRG: 0.697 Sensitivity CentroidHomfold‑LAST: 0.629 PknotsRG: 0.718 Positive Predictive Value CentroidHomfold‑LAST: 0.803 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 5.3419901105e-07	= CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAfold: 0.702 Sensitivity CentroidHomfold‑LAST: 0.629 RNAfold: 0.713 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAfold: 0.696 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.0200535500971	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAshapes: 0.667 Sensitivity CentroidHomfold‑LAST: 0.629 RNAshapes: 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 Fold: 0.642 Sensitivity CentroidHomfold‑LAST: 0.629 Fold: 0.667 Positive Predictive Value CentroidHomfold‑LAST: 0.803 Fold: 0.626 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.666 CentroidHomfold‑LAST: 0.649 Sensitivity TurboFold(seed): 0.635 CentroidHomfold‑LAST: 0.618 Positive Predictive Value TurboFold(seed): 0.708 CentroidHomfold‑LAST: 0.692 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.8740818951e-06	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.705 Afold: 0.679 Sensitivity CentroidHomfold‑LAST: 0.621 Afold: 0.704 Positive Predictive Value CentroidHomfold‑LAST: 0.810 Afold: 0.663 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.12734318562e-06	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Carnac(20): 0.656 Sensitivity CentroidHomfold‑LAST: 0.744 Carnac(20): 0.515 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Carnac(20): 0.845 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 RSpredict(20): 0.642 Sensitivity CentroidHomfold‑LAST: 0.726 RSpredict(20): 0.588 Positive Predictive Value CentroidHomfold‑LAST: 0.731 RSpredict(20): 0.708 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAsubopt: 0.667 Sensitivity CentroidHomfold‑LAST: 0.629 RNAsubopt: 0.692 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAsubopt: 0.649 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.695 Cylofold: 0.631 Sensitivity CentroidHomfold‑LAST: 0.623 Cylofold: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.785 Cylofold: 0.653 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 McQFold: 0.639 Sensitivity CentroidHomfold‑LAST: 0.629 McQFold: 0.643 Positive Predictive Value CentroidHomfold‑LAST: 0.803 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.677 RNASLOpt: 0.605 Sensitivity CentroidHomfold‑LAST: 0.601 RNASLOpt: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.767 RNASLOpt: 0.643 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.771 Pknots: 0.666 Sensitivity CentroidHomfold‑LAST: 0.719 Pknots: 0.679 Positive Predictive Value CentroidHomfold‑LAST: 0.835 Pknots: 0.664 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.758 CRWrnafold: 0.674 Sensitivity CentroidHomfold‑LAST: 0.670 CRWrnafold: 0.681 Positive Predictive Value CentroidHomfold‑LAST: 0.866 CRWrnafold: 0.679 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Multilign(20): 0.699 Sensitivity CentroidHomfold‑LAST: 0.744 Multilign(20): 0.688 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.30549897711e-08	? CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 RNASampler(seed): 0.579 Sensitivity CentroidHomfold‑LAST: 0.620 RNASampler(seed): 0.465 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.810 Alterna: 0.711 Sensitivity CentroidHomfold‑LAST: 0.719 Alterna: 0.734 Positive Predictive Value CentroidHomfold‑LAST: 0.922 Alterna: 0.704 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Mastr(20): 0.657 Sensitivity CentroidHomfold‑LAST: 0.744 Mastr(20): 0.553 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.740 Vsfold4: 0.604 Sensitivity CentroidHomfold‑LAST: 0.667 Vsfold4: 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.828 Vsfold4: 0.629 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Murlet(seed): 0.503 Sensitivity CentroidHomfold‑LAST: 0.617 Murlet(seed): 0.352 Positive Predictive Value CentroidHomfold‑LAST: 0.672 Murlet(seed): 0.736 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 MCFold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.696 MCFold: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.785 MCFold: 0.556 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.706 Vsfold5: 0.531 Sensitivity CentroidHomfold‑LAST: 0.642 Vsfold5: 0.538 Positive Predictive Value CentroidHomfold‑LAST: 0.786 Vsfold5: 0.539 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.699 RNAwolf: 0.483 Sensitivity CentroidHomfold‑LAST: 0.637 RNAwolf: 0.494 Positive Predictive Value CentroidHomfold‑LAST: 0.773 RNAwolf: 0.483 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.691 CMfinder(20): 0.652 Sensitivity CentroidHomfold‑LAST: 0.737 CMfinder(20): 0.518 Positive Predictive Value CentroidHomfold‑LAST: 0.656 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.752 NanoFolder: 0.374 Sensitivity CentroidHomfold‑LAST: 0.698 NanoFolder: 0.463 Positive Predictive Value CentroidHomfold‑LAST: 0.816 NanoFolder: 0.317 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.798 RDfolder: 0.611 Sensitivity CentroidHomfold‑LAST: 0.727 RDfolder: 0.560 Positive Predictive Value CentroidHomfold‑LAST: 0.887 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 RSpredict(seed): 0.171 Sensitivity CentroidHomfold‑LAST: 0.710 RSpredict(seed): 0.087 Positive Predictive Value CentroidHomfold‑LAST: 0.725 RSpredict(seed): 0.356 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.687 Multilign(seed): 0.672 Sensitivity CentroidHomfold‑LAST: 0.654 Multilign(seed): 0.615 Positive Predictive Value CentroidHomfold‑LAST: 0.736 Multilign(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.719 PPfold(seed): 0.091 Sensitivity CentroidHomfold‑LAST: 0.705 PPfold(seed): 0.016 Positive Predictive Value CentroidHomfold‑LAST: 0.741 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.660 Carnac(seed): 0.273 Sensitivity CentroidHomfold‑LAST: 0.638 Carnac(seed): 0.076 Positive Predictive Value CentroidHomfold‑LAST: 0.693 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.728 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.715 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.749 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	? CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CentroidHomfold‑LAST: 0.720 Sensitivity PETfold_2.0(seed): 0.889 CentroidHomfold‑LAST: 0.667 Positive Predictive Value PETfold_2.0(seed): 0.923 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidHomfold‑LAST: 0.720 Sensitivity PETfold_2.0(20): 0.889 CentroidHomfold‑LAST: 0.667 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Contrafold	39 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Contrafold: 0.649 Sensitivity CentroidAlifold(20): 0.728 Contrafold: 0.675 Positive Predictive Value CentroidAlifold(20): 0.901 Contrafold: 0.631 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Contrafold: 0.689 Sensitivity PETfold_pre2.0(seed): 0.841 Contrafold: 0.703 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Contrafold: 0.677 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.680 Contrafold: 0.592 Sensitivity ContextFold: 0.671 Contrafold: 0.607 Positive Predictive Value ContextFold: 0.689 Contrafold: 0.580 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.786 Contrafold: 0.707 Sensitivity MXScarna(seed): 0.749 Contrafold: 0.727 Positive Predictive Value MXScarna(seed): 0.825 Contrafold: 0.690 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.790 Contrafold: 0.664 Sensitivity RNAalifold(20): 0.704 Contrafold: 0.681 Positive Predictive Value RNAalifold(20): 0.891 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Contrafold: 0.627 Sensitivity PETfold_pre2.0(20): 0.776 Contrafold: 0.657 Positive Predictive Value PETfold_pre2.0(20): 0.815 Contrafold: 0.607 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.812 Contrafold: 0.701 Sensitivity PPfold(20): 0.753 Contrafold: 0.702 Positive Predictive Value PPfold(20): 0.880 Contrafold: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	57 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.675 Contrafold: 0.607 Sensitivity IPknot: 0.645 Contrafold: 0.621 Positive Predictive Value IPknot: 0.707 Contrafold: 0.594 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.755 Contrafold: 0.664 Sensitivity MXScarna(20): 0.720 Contrafold: 0.681 Positive Predictive Value MXScarna(20): 0.796 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.751 Contrafold: 0.664 Sensitivity RNASampler(20): 0.663 Contrafold: 0.681 Positive Predictive Value RNASampler(20): 0.856 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.773 Contrafold: 0.701 Sensitivity TurboFold(20): 0.737 Contrafold: 0.702 Positive Predictive Value TurboFold(20): 0.817 Contrafold: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	61 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Contrafold: 0.699 Sensitivity CentroidAlifold(seed): 0.602 Contrafold: 0.722 Positive Predictive Value CentroidAlifold(seed): 0.894 Contrafold: 0.678 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.85233844192e-08	137 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.667 Contrafold: 0.649 Sensitivity CentroidFold: 0.661 Contrafold: 0.675 Positive Predictive Value CentroidFold: 0.675 Contrafold: 0.625 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.662 Sfold: 0.613 Sensitivity Contrafold: 0.684 Sfold: 0.614 Positive Predictive Value Contrafold: 0.640 Sfold: 0.612 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 Contrafold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Contrafold: 0.714 CentroidHomfold‑LAST: 0.708 Sensitivity Contrafold: 0.728 CentroidHomfold‑LAST: 0.629 Positive Predictive Value Contrafold: 0.706 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.000218715568349		- RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.740 Contrafold: 0.699 Sensitivity RNAalifold(seed): 0.624 Contrafold: 0.716 Positive Predictive Value RNAalifold(seed): 0.879 Contrafold: 0.684 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.27481660653e-07	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.676 MaxExpect: 0.663 Sensitivity Contrafold: 0.693 MaxExpect: 0.679 Positive Predictive Value Contrafold: 0.662 MaxExpect: 0.648 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.1569883686e-08	= HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.737 Contrafold: 0.734 Sensitivity HotKnots: 0.761 Contrafold: 0.755 Positive Predictive Value HotKnots: 0.719 Contrafold: 0.720 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00385390231177	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.662 UNAFold: 0.589 Sensitivity Contrafold: 0.684 UNAFold: 0.620 Positive Predictive Value Contrafold: 0.640 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.652 ProbKnot: 0.638 Sensitivity Contrafold: 0.671 ProbKnot: 0.668 Positive Predictive Value Contrafold: 0.634 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 7.5939721025e-08	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.693 Contrafold: 0.664 Sensitivity Murlet(20): 0.594 Contrafold: 0.681 Positive Predictive Value Murlet(20): 0.815 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.658 PknotsRG: 0.575 Sensitivity Contrafold: 0.681 PknotsRG: 0.613 Positive Predictive Value Contrafold: 0.636 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.662 RNAfold: 0.583 Sensitivity Contrafold: 0.684 RNAfold: 0.619 Positive Predictive Value Contrafold: 0.640 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.734 RNAshapes: 0.714 Sensitivity Contrafold: 0.755 RNAshapes: 0.731 Positive Predictive Value Contrafold: 0.720 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.668 Fold: 0.636 Sensitivity Contrafold: 0.687 Fold: 0.668 Positive Predictive Value Contrafold: 0.652 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.648 TurboFold(seed): 0.647 Sensitivity Contrafold: 0.634 TurboFold(seed): 0.615 Positive Predictive Value Contrafold: 0.672 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.14664306206	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.651 Afold: 0.564 Sensitivity Contrafold: 0.676 Afold: 0.605 Positive Predictive Value Contrafold: 0.628 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.686 Contrafold: 0.664 Sensitivity Carnac(20): 0.518 Contrafold: 0.681 Positive Predictive Value Carnac(20): 0.915 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.660 Contrafold: 0.650 Sensitivity RSpredict(20): 0.597 Contrafold: 0.676 Positive Predictive Value RSpredict(20): 0.735 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000108348164592	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.734 RNAsubopt: 0.703 Sensitivity Contrafold: 0.755 RNAsubopt: 0.730 Positive Predictive Value Contrafold: 0.720 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.780 Cylofold: 0.701 Sensitivity Contrafold: 0.789 Cylofold: 0.686 Positive Predictive Value Contrafold: 0.779 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.661 McQFold: 0.501 Sensitivity Contrafold: 0.683 McQFold: 0.483 Positive Predictive Value Contrafold: 0.639 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.664 RNASLOpt: 0.580 Sensitivity Contrafold: 0.684 RNASLOpt: 0.559 Positive Predictive Value Contrafold: 0.651 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.775 Pknots: 0.705 Sensitivity Contrafold: 0.785 Pknots: 0.732 Positive Predictive Value Contrafold: 0.772 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.733 CRWrnafold: 0.683 Sensitivity Contrafold: 0.731 CRWrnafold: 0.690 Positive Predictive Value Contrafold: 0.745 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.673 Multilign(20): 0.652 Sensitivity Contrafold: 0.675 Multilign(20): 0.624 Positive Predictive Value Contrafold: 0.680 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.58152010255e-08	+ Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.779 RNASampler(seed): 0.728 Sensitivity Contrafold: 0.791 RNASampler(seed): 0.634 Positive Predictive Value Contrafold: 0.772 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.845 Alterna: 0.767 Sensitivity Contrafold: 0.840 Alterna: 0.777 Positive Predictive Value Contrafold: 0.857 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.664 Mastr(20): 0.620 Sensitivity Contrafold: 0.681 Mastr(20): 0.473 Positive Predictive Value Contrafold: 0.654 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.753 Vsfold4: 0.635 Sensitivity Contrafold: 0.770 Vsfold4: 0.625 Positive Predictive Value Contrafold: 0.742 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.750 Murlet(seed): 0.594 Sensitivity Contrafold: 0.750 Murlet(seed): 0.418 Positive Predictive Value Contrafold: 0.758 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.748 MCFold: 0.622 Sensitivity Contrafold: 0.766 MCFold: 0.663 Positive Predictive Value Contrafold: 0.740 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.759 Vsfold5: 0.593 Sensitivity Contrafold: 0.776 Vsfold5: 0.595 Positive Predictive Value Contrafold: 0.750 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.609 RNAwolf: 0.436 Sensitivity Contrafold: 0.627 RNAwolf: 0.446 Positive Predictive Value Contrafold: 0.593 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.735 CMfinder(20): 0.652 Sensitivity Contrafold: 0.746 CMfinder(20): 0.518 Positive Predictive Value Contrafold: 0.733 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.687 NanoFolder: 0.394 Sensitivity Contrafold: 0.703 NanoFolder: 0.485 Positive Predictive Value Contrafold: 0.679 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.835 RDfolder: 0.677 Sensitivity Contrafold: 0.829 RDfolder: 0.637 Positive Predictive Value Contrafold: 0.849 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.700 RSpredict(seed): 0.449 Sensitivity Contrafold: 0.724 RSpredict(seed): 0.304 Positive Predictive Value Contrafold: 0.679 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.699 Multilign(seed): 0.649 Sensitivity Contrafold: 0.678 Multilign(seed): 0.591 Positive Predictive Value Contrafold: 0.731 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.706 PPfold(seed): 0.094 Sensitivity Contrafold: 0.700 PPfold(seed): 0.019 Positive Predictive Value Contrafold: 0.719 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.738 Carnac(seed): 0.474 Sensitivity Contrafold: 0.747 Carnac(seed): 0.239 Positive Predictive Value Contrafold: 0.731 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.701 Mastr(seed): 0.279 Sensitivity Contrafold: 0.725 Mastr(seed): 0.088 Positive Predictive Value Contrafold: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Contrafold: 0.853 Sensitivity PETfold_2.0(seed): 0.845 Contrafold: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 Contrafold: 0.847 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Contrafold: 0.725 Sensitivity PETfold_2.0(20): 0.889 Contrafold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 Contrafold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAalifold(seed)	21 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.714 RNAalifold(seed): 0.663 Sensitivity CentroidAlifold(20): 0.588 RNAalifold(seed): 0.475 Positive Predictive Value CentroidAlifold(20): 0.871 RNAalifold(seed): 0.932 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	14 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.826 RNAalifold(seed): 0.767 Sensitivity PETfold_pre2.0(seed): 0.794 RNAalifold(seed): 0.670 Positive Predictive Value PETfold_pre2.0(seed): 0.860 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	10 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.796 RNAalifold(seed): 0.785 Sensitivity ContextFold: 0.770 RNAalifold(seed): 0.708 Positive Predictive Value ContextFold: 0.823 RNAalifold(seed): 0.872 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.39974817869e-07	34 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.749 RNAalifold(seed): 0.740 Sensitivity MXScarna(seed): 0.710 RNAalifold(seed): 0.624 Positive Predictive Value MXScarna(seed): 0.792 RNAalifold(seed): 0.879 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.03703286746e-07	20 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.692 RNAalifold(seed): 0.672 Sensitivity RNAalifold(20): 0.583 RNAalifold(seed): 0.488 Positive Predictive Value RNAalifold(20): 0.827 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23907313115e-07	8 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.643 PETfold_pre2.0(20): 0.547 Sensitivity RNAalifold(seed): 0.416 PETfold_pre2.0(20): 0.518 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.585 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.683 PPfold(20): 0.681 Sensitivity RNAalifold(seed): 0.502 PPfold(20): 0.596 Positive Predictive Value RNAalifold(seed): 0.936 PPfold(20): 0.786 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.781 IPknot: 0.721 Sensitivity RNAalifold(seed): 0.701 IPknot: 0.689 Positive Predictive Value RNAalifold(seed): 0.870 IPknot: 0.754 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.49381627234e-08	20 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 RNAalifold(seed): 0.672 Sensitivity MXScarna(20): 0.644 RNAalifold(seed): 0.488 Positive Predictive Value MXScarna(20): 0.741 RNAalifold(seed): 0.931 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.19220141104e-07	20 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 RNASampler(20): 0.671 Sensitivity RNAalifold(seed): 0.488 RNASampler(20): 0.575 Positive Predictive Value RNAalifold(seed): 0.931 RNASampler(20): 0.789 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.000699240967729	9 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.691 RNAalifold(seed): 0.683 Sensitivity TurboFold(20): 0.645 RNAalifold(seed): 0.502 Positive Predictive Value TurboFold(20): 0.749 RNAalifold(seed): 0.936 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	37 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 RNAalifold(seed): 0.734 Sensitivity CentroidAlifold(seed): 0.702 RNAalifold(seed): 0.612 Positive Predictive Value CentroidAlifold(seed): 0.881 RNAalifold(seed): 0.882 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.734 CentroidFold: 0.708 Sensitivity RNAalifold(seed): 0.612 CentroidFold: 0.702 Positive Predictive Value RNAalifold(seed): 0.882 CentroidFold: 0.715 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.000218715568349	34 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.740 Sfold: 0.659 Sensitivity RNAalifold(seed): 0.624 Sfold: 0.653 Positive Predictive Value RNAalifold(seed): 0.879 Sfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.10039559051e-07	11 RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.664 CentroidHomfold‑LAST: 0.638 Sensitivity RNAalifold(seed): 0.518 CentroidHomfold‑LAST: 0.617 Positive Predictive Value RNAalifold(seed): 0.862 CentroidHomfold‑LAST: 0.672 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.81480685939e-07	34 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.740 Contrafold: 0.699 Sensitivity RNAalifold(seed): 0.624 Contrafold: 0.716 Positive Predictive Value RNAalifold(seed): 0.879 Contrafold: 0.684 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.27481660653e-07		+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.740 MaxExpect: 0.643 Sensitivity RNAalifold(seed): 0.627 MaxExpect: 0.660 Positive Predictive Value RNAalifold(seed): 0.876 MaxExpect: 0.628 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.680 HotKnots: 0.659 Sensitivity RNAalifold(seed): 0.525 HotKnots: 0.697 Positive Predictive Value RNAalifold(seed): 0.885 HotKnots: 0.629 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.03703286746e-07	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.740 UNAFold: 0.632 Sensitivity RNAalifold(seed): 0.624 UNAFold: 0.653 Positive Predictive Value RNAalifold(seed): 0.879 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.713 ProbKnot: 0.600 Sensitivity RNAalifold(seed): 0.593 ProbKnot: 0.624 Positive Predictive Value RNAalifold(seed): 0.860 ProbKnot: 0.579 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Murlet(20): 0.595 Sensitivity RNAalifold(seed): 0.488 Murlet(20): 0.477 Positive Predictive Value RNAalifold(seed): 0.931 Murlet(20): 0.749 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	= RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.680 PknotsRG: 0.677 Sensitivity RNAalifold(seed): 0.525 PknotsRG: 0.711 Positive Predictive Value RNAalifold(seed): 0.885 PknotsRG: 0.650 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.935722063919	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.740 RNAfold: 0.639 Sensitivity RNAalifold(seed): 0.624 RNAfold: 0.664 Positive Predictive Value RNAalifold(seed): 0.879 RNAfold: 0.617 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	= RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.683 RNAalifold(seed): 0.680 Sensitivity RNAshapes: 0.707 RNAalifold(seed): 0.525 Positive Predictive Value RNAshapes: 0.666 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.090340659959	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.733 Fold: 0.609 Sensitivity RNAalifold(seed): 0.617 Fold: 0.639 Positive Predictive Value RNAalifold(seed): 0.871 Fold: 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	= RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.617 TurboFold(seed): 0.611 Sensitivity RNAalifold(seed): 0.462 TurboFold(seed): 0.578 Positive Predictive Value RNAalifold(seed): 0.832 TurboFold(seed): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.106641111385	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.675 RNAalifold(seed): 0.644 Sensitivity Afold: 0.714 RNAalifold(seed): 0.491 Positive Predictive Value Afold: 0.642 RNAalifold(seed): 0.850 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Carnac(20): 0.596 Sensitivity RNAalifold(seed): 0.488 Carnac(20): 0.385 Positive Predictive Value RNAalifold(seed): 0.931 Carnac(20): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.662 RSpredict(20): 0.526 Sensitivity RNAalifold(seed): 0.472 RSpredict(20): 0.465 Positive Predictive Value RNAalifold(seed): 0.932 RSpredict(20): 0.602 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.680 RNAsubopt: 0.651 Sensitivity RNAalifold(seed): 0.525 RNAsubopt: 0.682 Positive Predictive Value RNAalifold(seed): 0.885 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.85233844192e-08	= Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.666 RNAalifold(seed): 0.664 Sensitivity Cylofold: 0.647 RNAalifold(seed): 0.510 Positive Predictive Value Cylofold: 0.696 RNAalifold(seed): 0.876 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.456379442218	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.740 McQFold: 0.623 Sensitivity RNAalifold(seed): 0.624 McQFold: 0.635 Positive Predictive Value RNAalifold(seed): 0.879 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNASLOpt: 0.490 Sensitivity RNAalifold(seed): 0.464 RNASLOpt: 0.474 Positive Predictive Value RNAalifold(seed): 0.875 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.725 Pknots: 0.690 Sensitivity RNAalifold(seed): 0.578 Pknots: 0.722 Positive Predictive Value RNAalifold(seed): 0.916 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 6.53888633552e-08	? RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.679 Multilign(20): 0.500 Sensitivity RNAalifold(seed): 0.498 Multilign(20): 0.464 Positive Predictive Value RNAalifold(seed): 0.937 Multilign(20): 0.554 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	- RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 RNAalifold(seed): 0.714 Sensitivity RNASampler(seed): 0.634 RNAalifold(seed): 0.585 Positive Predictive Value RNASampler(seed): 0.843 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	- Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.844 RNAalifold(seed): 0.743 Sensitivity Alterna: 0.833 RNAalifold(seed): 0.644 Positive Predictive Value Alterna: 0.863 RNAalifold(seed): 0.869 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Mastr(20): 0.462 Sensitivity RNAalifold(seed): 0.488 Mastr(20): 0.278 Positive Predictive Value RNAalifold(seed): 0.931 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.682 Vsfold4: 0.574 Sensitivity RNAalifold(seed): 0.530 Vsfold4: 0.575 Positive Predictive Value RNAalifold(seed): 0.883 Vsfold4: 0.581 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.733 Murlet(seed): 0.594 Sensitivity RNAalifold(seed): 0.591 Murlet(seed): 0.418 Positive Predictive Value RNAalifold(seed): 0.916 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.703 MCFold: 0.569 Sensitivity RNAalifold(seed): 0.549 MCFold: 0.616 Positive Predictive Value RNAalifold(seed): 0.905 MCFold: 0.536 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.686 Vsfold5: 0.550 Sensitivity RNAalifold(seed): 0.535 Vsfold5: 0.552 Positive Predictive Value RNAalifold(seed): 0.884 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.764 RNAwolf: 0.494 Sensitivity RNAalifold(seed): 0.667 RNAwolf: 0.497 Positive Predictive Value RNAalifold(seed): 0.876 RNAwolf: 0.493 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.839 CMfinder(20): 0.536 Sensitivity RNAalifold(seed): 0.708 CMfinder(20): 0.292 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.581 NanoFolder: 0.294 Sensitivity RNAalifold(seed): 0.426 NanoFolder: 0.357 Positive Predictive Value RNAalifold(seed): 0.803 NanoFolder: 0.259 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.740 RDfolder: 0.644 Sensitivity RNAalifold(seed): 0.624 RDfolder: 0.592 Positive Predictive Value RNAalifold(seed): 0.889 RDfolder: 0.717 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.733 RSpredict(seed): 0.553 Sensitivity RNAalifold(seed): 0.610 RSpredict(seed): 0.419 Positive Predictive Value RNAalifold(seed): 0.883 RSpredict(seed): 0.733 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 RNAalifold(seed): 0.641 Sensitivity Multilign(seed): 0.591 RNAalifold(seed): 0.500 Positive Predictive Value Multilign(seed): 0.724 RNAalifold(seed): 0.832 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.653 PPfold(seed): 0.124 Sensitivity RNAalifold(seed): 0.496 PPfold(seed): 0.034 Positive Predictive Value RNAalifold(seed): 0.868 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.780 Carnac(seed): 0.499 Sensitivity RNAalifold(seed): 0.680 Carnac(seed): 0.264 Positive Predictive Value RNAalifold(seed): 0.895 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.680 Mastr(seed): 0.345 Sensitivity RNAalifold(seed): 0.525 Mastr(seed): 0.134 Positive Predictive Value RNAalifold(seed): 0.885 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 RNAalifold(seed): 0.780 Sensitivity PETfold_2.0(seed): 0.806 RNAalifold(seed): 0.613 Positive Predictive Value PETfold_2.0(seed): 0.862 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MaxExpect	39 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.808 MaxExpect: 0.667 Sensitivity CentroidAlifold(20): 0.728 MaxExpect: 0.681 Positive Predictive Value CentroidAlifold(20): 0.901 MaxExpect: 0.661 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 MaxExpect: 0.617 Sensitivity PETfold_pre2.0(seed): 0.841 MaxExpect: 0.627 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MaxExpect: 0.609 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	49 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.680 MaxExpect: 0.572 Sensitivity ContextFold: 0.671 MaxExpect: 0.588 Positive Predictive Value ContextFold: 0.689 MaxExpect: 0.557 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.781 MaxExpect: 0.676 Sensitivity MXScarna(seed): 0.746 MaxExpect: 0.690 Positive Predictive Value MXScarna(seed): 0.819 MaxExpect: 0.664 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.787 MaxExpect: 0.690 Sensitivity RNAalifold(20): 0.701 MaxExpect: 0.693 Positive Predictive Value RNAalifold(20): 0.887 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 MaxExpect: 0.592 Sensitivity PETfold_pre2.0(20): 0.776 MaxExpect: 0.609 Positive Predictive Value PETfold_pre2.0(20): 0.815 MaxExpect: 0.585 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.812 MaxExpect: 0.666 Sensitivity PPfold(20): 0.753 MaxExpect: 0.656 Positive Predictive Value PPfold(20): 0.880 MaxExpect: 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	57 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.675 MaxExpect: 0.583 Sensitivity IPknot: 0.645 MaxExpect: 0.600 Positive Predictive Value IPknot: 0.707 MaxExpect: 0.569 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.751 MaxExpect: 0.690 Sensitivity MXScarna(20): 0.715 MaxExpect: 0.693 Positive Predictive Value MXScarna(20): 0.794 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.749 MaxExpect: 0.690 Sensitivity RNASampler(20): 0.663 MaxExpect: 0.693 Positive Predictive Value RNASampler(20): 0.851 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.773 MaxExpect: 0.666 Sensitivity TurboFold(20): 0.737 MaxExpect: 0.656 Positive Predictive Value TurboFold(20): 0.817 MaxExpect: 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	58 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.735 MaxExpect: 0.672 Sensitivity CentroidAlifold(seed): 0.606 MaxExpect: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.892 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.85233844192e-08	130 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.693 MaxExpect: 0.660 Sensitivity CentroidFold: 0.679 MaxExpect: 0.677 Positive Predictive Value CentroidFold: 0.708 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.663 Sfold: 0.649 Sensitivity MaxExpect: 0.679 Sfold: 0.645 Positive Predictive Value MaxExpect: 0.648 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.000243049897693	56 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 MaxExpect: 0.669 Sensitivity CentroidHomfold‑LAST: 0.629 MaxExpect: 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.803 MaxExpect: 0.665 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.676 MaxExpect: 0.663 Sensitivity Contrafold: 0.693 MaxExpect: 0.679 Positive Predictive Value Contrafold: 0.662 MaxExpect: 0.648 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.1569883686e-08	32 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.740 MaxExpect: 0.643 Sensitivity RNAalifold(seed): 0.627 MaxExpect: 0.660 Positive Predictive Value RNAalifold(seed): 0.876 MaxExpect: 0.628 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08		- HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.728 MaxExpect: 0.717 Sensitivity HotKnots: 0.755 MaxExpect: 0.733 Positive Predictive Value HotKnots: 0.707 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.26115971074e-07	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.663 UNAFold: 0.630 Sensitivity MaxExpect: 0.679 UNAFold: 0.652 Positive Predictive Value MaxExpect: 0.648 UNAFold: 0.610 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.643 ProbKnot: 0.638 Sensitivity MaxExpect: 0.663 ProbKnot: 0.668 Positive Predictive Value MaxExpect: 0.626 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.690 Murlet(20): 0.688 Sensitivity MaxExpect: 0.693 Murlet(20): 0.590 Positive Predictive Value MaxExpect: 0.694 Murlet(20): 0.809 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0186613811547	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.670 PknotsRG: 0.616 Sensitivity MaxExpect: 0.685 PknotsRG: 0.646 Positive Predictive Value MaxExpect: 0.656 PknotsRG: 0.589 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.663 RNAfold: 0.621 Sensitivity MaxExpect: 0.679 RNAfold: 0.647 Positive Predictive Value MaxExpect: 0.648 RNAfold: 0.597 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.717 RNAshapes: 0.709 Sensitivity MaxExpect: 0.733 RNAshapes: 0.728 Positive Predictive Value MaxExpect: 0.707 RNAshapes: 0.697 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.03703286746e-07	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.655 Fold: 0.636 Sensitivity MaxExpect: 0.673 Fold: 0.668 Positive Predictive Value MaxExpect: 0.638 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.85233844192e-08	- TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.647 MaxExpect: 0.600 Sensitivity TurboFold(seed): 0.615 MaxExpect: 0.580 Positive Predictive Value TurboFold(seed): 0.691 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.88760648134e-09	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.662 Afold: 0.606 Sensitivity MaxExpect: 0.681 Afold: 0.638 Positive Predictive Value MaxExpect: 0.644 Afold: 0.578 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.690 Carnac(20): 0.684 Sensitivity MaxExpect: 0.693 Carnac(20): 0.516 Positive Predictive Value MaxExpect: 0.694 Carnac(20): 0.912 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.00217949791134	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.666 RSpredict(20): 0.657 Sensitivity MaxExpect: 0.679 RSpredict(20): 0.595 Positive Predictive Value MaxExpect: 0.660 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.000207424631753	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.717 RNAsubopt: 0.699 Sensitivity MaxExpect: 0.733 RNAsubopt: 0.729 Positive Predictive Value MaxExpect: 0.707 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.753 Cylofold: 0.701 Sensitivity MaxExpect: 0.757 Cylofold: 0.686 Positive Predictive Value MaxExpect: 0.757 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.662 McQFold: 0.542 Sensitivity MaxExpect: 0.678 McQFold: 0.550 Positive Predictive Value MaxExpect: 0.647 McQFold: 0.536 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.635 RNASLOpt: 0.580 Sensitivity MaxExpect: 0.645 RNASLOpt: 0.559 Positive Predictive Value MaxExpect: 0.632 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.768 Pknots: 0.699 Sensitivity MaxExpect: 0.772 Pknots: 0.726 Positive Predictive Value MaxExpect: 0.772 Pknots: 0.682 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.683 MaxExpect: 0.662 Sensitivity CRWrnafold: 0.690 MaxExpect: 0.667 Positive Predictive Value CRWrnafold: 0.689 MaxExpect: 0.669 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.10039559051e-07	- Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.652 MaxExpect: 0.634 Sensitivity Multilign(20): 0.624 MaxExpect: 0.635 Positive Predictive Value Multilign(20): 0.692 MaxExpect: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.747 RNASampler(seed): 0.717 Sensitivity MaxExpect: 0.766 RNASampler(seed): 0.627 Positive Predictive Value MaxExpect: 0.736 RNASampler(seed): 0.827 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.53384937367e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.815 Alterna: 0.750 Sensitivity MaxExpect: 0.815 Alterna: 0.764 Positive Predictive Value MaxExpect: 0.823 Alterna: 0.749 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.690 Mastr(20): 0.612 Sensitivity MaxExpect: 0.693 Mastr(20): 0.463 Positive Predictive Value MaxExpect: 0.694 Mastr(20): 0.817 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.741 Vsfold4: 0.627 Sensitivity MaxExpect: 0.754 Vsfold4: 0.619 Positive Predictive Value MaxExpect: 0.734 Vsfold4: 0.646 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.708 Murlet(seed): 0.593 Sensitivity MaxExpect: 0.705 Murlet(seed): 0.420 Positive Predictive Value MaxExpect: 0.720 Murlet(seed): 0.848 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.740 MCFold: 0.599 Sensitivity MaxExpect: 0.751 MCFold: 0.640 Positive Predictive Value MaxExpect: 0.736 MCFold: 0.572 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.731 Vsfold5: 0.578 Sensitivity MaxExpect: 0.744 Vsfold5: 0.579 Positive Predictive Value MaxExpect: 0.725 Vsfold5: 0.588 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.588 RNAwolf: 0.436 Sensitivity MaxExpect: 0.606 RNAwolf: 0.446 Positive Predictive Value MaxExpect: 0.571 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.653 CMfinder(20): 0.652 Sensitivity MaxExpect: 0.640 CMfinder(20): 0.518 Positive Predictive Value MaxExpect: 0.676 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.690 NanoFolder: 0.394 Sensitivity MaxExpect: 0.701 NanoFolder: 0.485 Positive Predictive Value MaxExpect: 0.687 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.801 RDfolder: 0.668 Sensitivity MaxExpect: 0.799 RDfolder: 0.625 Positive Predictive Value MaxExpect: 0.812 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.671 RSpredict(seed): 0.448 Sensitivity MaxExpect: 0.688 RSpredict(seed): 0.305 Positive Predictive Value MaxExpect: 0.657 RSpredict(seed): 0.661 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.674 Multilign(seed): 0.649 Sensitivity MaxExpect: 0.635 Multilign(seed): 0.591 Positive Predictive Value MaxExpect: 0.725 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.638 PPfold(seed): 0.094 Sensitivity MaxExpect: 0.623 PPfold(seed): 0.019 Positive Predictive Value MaxExpect: 0.663 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.688 Carnac(seed): 0.473 Sensitivity MaxExpect: 0.694 Carnac(seed): 0.239 Positive Predictive Value MaxExpect: 0.683 Carnac(seed): 0.941 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.699 Mastr(seed): 0.291 Sensitivity MaxExpect: 0.711 Mastr(seed): 0.095 Positive Predictive Value MaxExpect: 0.692 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 MaxExpect: 0.845 Sensitivity PETfold_2.0(seed): 0.845 MaxExpect: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 MaxExpect: 0.833 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.905 MaxExpect: 0.712 Sensitivity PETfold_2.0(20): 0.889 MaxExpect: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 MaxExpect: 0.690 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
HotKnots	39 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.808 HotKnots: 0.645 Sensitivity CentroidAlifold(20): 0.728 HotKnots: 0.677 Positive Predictive Value CentroidAlifold(20): 0.901 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 HotKnots: 0.610 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.646 Positive Predictive Value PETfold_pre2.0(seed): 0.913 HotKnots: 0.584 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	47 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.760 HotKnots: 0.661 Sensitivity ContextFold: 0.742 HotKnots: 0.689 Positive Predictive Value ContextFold: 0.784 HotKnots: 0.640 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.769 HotKnots: 0.676 Sensitivity MXScarna(seed): 0.727 HotKnots: 0.706 Positive Predictive Value MXScarna(seed): 0.819 HotKnots: 0.653 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.790 HotKnots: 0.668 Sensitivity RNAalifold(20): 0.704 HotKnots: 0.692 Positive Predictive Value RNAalifold(20): 0.891 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 HotKnots: 0.588 Sensitivity PETfold_pre2.0(20): 0.776 HotKnots: 0.634 Positive Predictive Value PETfold_pre2.0(20): 0.815 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.57237423209e-08	15 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.812 HotKnots: 0.661 Sensitivity PPfold(20): 0.753 HotKnots: 0.686 Positive Predictive Value PPfold(20): 0.880 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	55 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.742 HotKnots: 0.673 Sensitivity IPknot: 0.729 HotKnots: 0.700 Positive Predictive Value IPknot: 0.759 HotKnots: 0.654 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.755 HotKnots: 0.668 Sensitivity MXScarna(20): 0.720 HotKnots: 0.692 Positive Predictive Value MXScarna(20): 0.796 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.751 HotKnots: 0.668 Sensitivity RNASampler(20): 0.663 HotKnots: 0.692 Positive Predictive Value RNASampler(20): 0.856 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.773 HotKnots: 0.661 Sensitivity TurboFold(20): 0.737 HotKnots: 0.686 Positive Predictive Value TurboFold(20): 0.817 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	60 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 HotKnots: 0.671 Sensitivity CentroidAlifold(seed): 0.535 HotKnots: 0.706 Positive Predictive Value CentroidAlifold(seed): 0.884 HotKnots: 0.645 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 4.57295429596e-06	133 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.737 HotKnots: 0.722 Sensitivity CentroidFold: 0.736 HotKnots: 0.752 Positive Predictive Value CentroidFold: 0.743 HotKnots: 0.700 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 4.48494289621e-08	135 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.755 HotKnots: 0.737 Sensitivity Sfold: 0.746 HotKnots: 0.761 Positive Predictive Value Sfold: 0.769 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.721 CentroidHomfold‑LAST: 0.708 Sensitivity HotKnots: 0.735 CentroidHomfold‑LAST: 0.629 Positive Predictive Value HotKnots: 0.712 CentroidHomfold‑LAST: 0.803 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.53079410487e-06	135 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.737 Contrafold: 0.734 Sensitivity HotKnots: 0.761 Contrafold: 0.755 Positive Predictive Value HotKnots: 0.719 Contrafold: 0.720 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00385390231177	33 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.680 HotKnots: 0.659 Sensitivity RNAalifold(seed): 0.525 HotKnots: 0.697 Positive Predictive Value RNAalifold(seed): 0.885 HotKnots: 0.629 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.03703286746e-07	115 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.728 MaxExpect: 0.717 Sensitivity HotKnots: 0.755 MaxExpect: 0.733 Positive Predictive Value HotKnots: 0.707 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.26115971074e-07		= UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.738 HotKnots: 0.737 Sensitivity UNAFold: 0.756 HotKnots: 0.761 Positive Predictive Value UNAFold: 0.727 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.0119532120069	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.711 ProbKnot: 0.698 Sensitivity HotKnots: 0.742 ProbKnot: 0.732 Positive Predictive Value HotKnots: 0.686 ProbKnot: 0.670 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 2.45033651981e-07	- Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.693 HotKnots: 0.668 Sensitivity Murlet(20): 0.594 HotKnots: 0.692 Positive Predictive Value Murlet(20): 0.815 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.59499054376e-07	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.737 PknotsRG: 0.718 Sensitivity HotKnots: 0.761 PknotsRG: 0.744 Positive Predictive Value HotKnots: 0.719 PknotsRG: 0.698 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.737 RNAfold: 0.726 Sensitivity HotKnots: 0.761 RNAfold: 0.747 Positive Predictive Value HotKnots: 0.719 RNAfold: 0.711 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.737 RNAshapes: 0.714 Sensitivity HotKnots: 0.761 RNAshapes: 0.731 Positive Predictive Value HotKnots: 0.719 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.728 Fold: 0.710 Sensitivity HotKnots: 0.758 Fold: 0.740 Positive Predictive Value HotKnots: 0.705 Fold: 0.687 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 8.81311508309e-08	- TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.647 HotKnots: 0.625 Sensitivity TurboFold(seed): 0.615 HotKnots: 0.653 Positive Predictive Value TurboFold(seed): 0.691 HotKnots: 0.609 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.88120811869e-05	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.745 Afold: 0.717 Sensitivity HotKnots: 0.774 Afold: 0.746 Positive Predictive Value HotKnots: 0.722 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.686 HotKnots: 0.668 Sensitivity Carnac(20): 0.518 HotKnots: 0.692 Positive Predictive Value Carnac(20): 0.915 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.3082811195e-06	- RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.660 HotKnots: 0.646 Sensitivity RSpredict(20): 0.597 HotKnots: 0.678 Positive Predictive Value RSpredict(20): 0.735 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.47427610203e-05	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.737 RNAsubopt: 0.703 Sensitivity HotKnots: 0.761 RNAsubopt: 0.730 Positive Predictive Value HotKnots: 0.719 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.756 Cylofold: 0.701 Sensitivity HotKnots: 0.772 Cylofold: 0.686 Positive Predictive Value HotKnots: 0.749 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.735 McQFold: 0.671 Sensitivity HotKnots: 0.760 McQFold: 0.677 Positive Predictive Value HotKnots: 0.717 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.661 RNASLOpt: 0.580 Sensitivity HotKnots: 0.689 RNASLOpt: 0.559 Positive Predictive Value HotKnots: 0.640 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.771 Pknots: 0.705 Sensitivity HotKnots: 0.787 Pknots: 0.732 Positive Predictive Value HotKnots: 0.763 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.725 CRWrnafold: 0.683 Sensitivity HotKnots: 0.747 CRWrnafold: 0.690 Positive Predictive Value HotKnots: 0.712 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.699 Multilign(20): 0.652 Sensitivity HotKnots: 0.707 Multilign(20): 0.624 Positive Predictive Value HotKnots: 0.701 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	- RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.728 HotKnots: 0.717 Sensitivity RNASampler(seed): 0.634 HotKnots: 0.762 Positive Predictive Value RNASampler(seed): 0.843 HotKnots: 0.683 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000512854650149	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.830 Alterna: 0.767 Sensitivity HotKnots: 0.835 Alterna: 0.777 Positive Predictive Value HotKnots: 0.833 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.668 Mastr(20): 0.620 Sensitivity HotKnots: 0.692 Mastr(20): 0.473 Positive Predictive Value HotKnots: 0.651 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.752 Vsfold4: 0.635 Sensitivity HotKnots: 0.774 Vsfold4: 0.625 Positive Predictive Value HotKnots: 0.738 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.710 Murlet(seed): 0.594 Sensitivity HotKnots: 0.730 Murlet(seed): 0.418 Positive Predictive Value HotKnots: 0.699 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.760 MCFold: 0.622 Sensitivity HotKnots: 0.785 MCFold: 0.663 Positive Predictive Value HotKnots: 0.743 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.747 Vsfold5: 0.593 Sensitivity HotKnots: 0.768 Vsfold5: 0.595 Positive Predictive Value HotKnots: 0.732 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.668 RNAwolf: 0.467 Sensitivity HotKnots: 0.699 RNAwolf: 0.481 Positive Predictive Value HotKnots: 0.644 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: 0.686 CMfinder(20): 0.652 Sensitivity HotKnots: 0.693 CMfinder(20): 0.518 Positive Predictive Value HotKnots: 0.687 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.692 NanoFolder: 0.394 Sensitivity HotKnots: 0.717 NanoFolder: 0.485 Positive Predictive Value HotKnots: 0.675 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.823 RDfolder: 0.677 Sensitivity HotKnots: 0.830 RDfolder: 0.637 Positive Predictive Value HotKnots: 0.824 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.672 RSpredict(seed): 0.316 Sensitivity HotKnots: 0.707 RSpredict(seed): 0.179 Positive Predictive Value HotKnots: 0.645 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.649 HotKnots: 0.581 Sensitivity Multilign(seed): 0.591 HotKnots: 0.596 Positive Predictive Value Multilign(seed): 0.724 HotKnots: 0.579 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.617 PPfold(seed): 0.094 Sensitivity HotKnots: 0.636 PPfold(seed): 0.019 Positive Predictive Value HotKnots: 0.609 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.732 Carnac(seed): 0.277 Sensitivity HotKnots: 0.751 Carnac(seed): 0.078 Positive Predictive Value HotKnots: 0.722 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.678 Mastr(seed): 0.279 Sensitivity HotKnots: 0.707 Mastr(seed): 0.088 Positive Predictive Value HotKnots: 0.656 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs PETfold_2.0(seed) Matthews Correlation Coefficient HotKnots: 0.868 PETfold_2.0(seed): 0.866 Sensitivity HotKnots: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value HotKnots: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.905 HotKnots: 0.752 Sensitivity PETfold_2.0(20): 0.889 HotKnots: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 HotKnots: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
UNAFold	39 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 UNAFold: 0.658 Sensitivity CentroidAlifold(20): 0.728 UNAFold: 0.678 Positive Predictive Value CentroidAlifold(20): 0.901 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 UNAFold: 0.572 Sensitivity PETfold_pre2.0(seed): 0.841 UNAFold: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.892 UNAFold: 0.557 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.680 UNAFold: 0.562 Sensitivity ContextFold: 0.671 UNAFold: 0.588 Positive Predictive Value ContextFold: 0.689 UNAFold: 0.540 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.786 UNAFold: 0.655 Sensitivity MXScarna(seed): 0.749 UNAFold: 0.673 Positive Predictive Value MXScarna(seed): 0.825 UNAFold: 0.640 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.790 UNAFold: 0.692 Sensitivity RNAalifold(20): 0.704 UNAFold: 0.701 Positive Predictive Value RNAalifold(20): 0.891 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 UNAFold: 0.572 Sensitivity PETfold_pre2.0(20): 0.776 UNAFold: 0.606 Positive Predictive Value PETfold_pre2.0(20): 0.815 UNAFold: 0.549 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	15 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.812 UNAFold: 0.661 Sensitivity PPfold(20): 0.753 UNAFold: 0.672 Positive Predictive Value PPfold(20): 0.880 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.21671975982e-08	57 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.675 UNAFold: 0.576 Sensitivity IPknot: 0.645 UNAFold: 0.600 Positive Predictive Value IPknot: 0.707 UNAFold: 0.554 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.755 UNAFold: 0.692 Sensitivity MXScarna(20): 0.720 UNAFold: 0.701 Positive Predictive Value MXScarna(20): 0.796 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.751 UNAFold: 0.692 Sensitivity RNASampler(20): 0.663 UNAFold: 0.701 Positive Predictive Value RNASampler(20): 0.856 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.773 UNAFold: 0.661 Sensitivity TurboFold(20): 0.737 UNAFold: 0.672 Positive Predictive Value TurboFold(20): 0.817 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	61 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 UNAFold: 0.649 Sensitivity CentroidAlifold(seed): 0.602 UNAFold: 0.670 Positive Predictive Value CentroidAlifold(seed): 0.894 UNAFold: 0.631 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.667 UNAFold: 0.600 Sensitivity CentroidFold: 0.661 UNAFold: 0.634 Positive Predictive Value CentroidFold: 0.675 UNAFold: 0.568 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.613 UNAFold: 0.589 Sensitivity Sfold: 0.614 UNAFold: 0.620 Positive Predictive Value Sfold: 0.612 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 UNAFold: 0.688 Sensitivity CentroidHomfold‑LAST: 0.629 UNAFold: 0.700 Positive Predictive Value CentroidHomfold‑LAST: 0.803 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 4.48494289621e-08	140 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.662 UNAFold: 0.589 Sensitivity Contrafold: 0.684 UNAFold: 0.620 Positive Predictive Value Contrafold: 0.640 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.740 UNAFold: 0.632 Sensitivity RNAalifold(seed): 0.624 UNAFold: 0.653 Positive Predictive Value RNAalifold(seed): 0.879 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	118 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.663 UNAFold: 0.630 Sensitivity MaxExpect: 0.679 UNAFold: 0.652 Positive Predictive Value MaxExpect: 0.648 UNAFold: 0.610 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.738 HotKnots: 0.737 Sensitivity UNAFold: 0.756 HotKnots: 0.761 Positive Predictive Value UNAFold: 0.727 HotKnots: 0.719 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.0119532120069		= ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.638 UNAFold: 0.636 Sensitivity ProbKnot: 0.668 UNAFold: 0.661 Positive Predictive Value ProbKnot: 0.612 UNAFold: 0.613 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.00586086047676	= Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.693 UNAFold: 0.692 Sensitivity Murlet(20): 0.594 UNAFold: 0.701 Positive Predictive Value Murlet(20): 0.815 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.183291550418	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.591 PknotsRG: 0.575 Sensitivity UNAFold: 0.623 PknotsRG: 0.613 Positive Predictive Value UNAFold: 0.561 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.589 RNAfold: 0.583 Sensitivity UNAFold: 0.620 RNAfold: 0.619 Positive Predictive Value UNAFold: 0.560 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.738 RNAshapes: 0.714 Sensitivity UNAFold: 0.756 RNAshapes: 0.731 Positive Predictive Value UNAFold: 0.727 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.653 Fold: 0.636 Sensitivity UNAFold: 0.677 Fold: 0.668 Positive Predictive Value UNAFold: 0.631 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 8.1815824276e-08	- TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.647 UNAFold: 0.579 Sensitivity TurboFold(seed): 0.615 UNAFold: 0.584 Positive Predictive Value TurboFold(seed): 0.691 UNAFold: 0.584 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.02533530638e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.569 Afold: 0.564 Sensitivity UNAFold: 0.605 Afold: 0.605 Positive Predictive Value UNAFold: 0.536 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.692 Carnac(20): 0.686 Sensitivity UNAFold: 0.701 Carnac(20): 0.518 Positive Predictive Value UNAFold: 0.689 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.58638884049e-05	= RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.660 UNAFold: 0.659 Sensitivity RSpredict(20): 0.597 UNAFold: 0.679 Positive Predictive Value RSpredict(20): 0.735 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.788063625903	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.738 RNAsubopt: 0.703 Sensitivity UNAFold: 0.756 RNAsubopt: 0.730 Positive Predictive Value UNAFold: 0.727 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.739 Cylofold: 0.701 Sensitivity UNAFold: 0.746 Cylofold: 0.686 Positive Predictive Value UNAFold: 0.741 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.588 McQFold: 0.501 Sensitivity UNAFold: 0.619 McQFold: 0.483 Positive Predictive Value UNAFold: 0.559 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.638 RNASLOpt: 0.580 Sensitivity UNAFold: 0.660 RNASLOpt: 0.559 Positive Predictive Value UNAFold: 0.623 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.778 Pknots: 0.705 Sensitivity UNAFold: 0.784 Pknots: 0.732 Positive Predictive Value UNAFold: 0.779 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.683 UNAFold: 0.683 Sensitivity CRWrnafold: 0.690 UNAFold: 0.694 Positive Predictive Value CRWrnafold: 0.689 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.706652010983	+ UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.666 Multilign(20): 0.652 Sensitivity UNAFold: 0.667 Multilign(20): 0.624 Positive Predictive Value UNAFold: 0.676 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.40027452735e-08	+ UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.740 RNASampler(seed): 0.728 Sensitivity UNAFold: 0.767 RNASampler(seed): 0.634 Positive Predictive Value UNAFold: 0.721 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.23248012054e-07	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.831 Alterna: 0.767 Sensitivity UNAFold: 0.829 Alterna: 0.777 Positive Predictive Value UNAFold: 0.842 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.692 Mastr(20): 0.620 Sensitivity UNAFold: 0.701 Mastr(20): 0.473 Positive Predictive Value UNAFold: 0.689 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.753 Vsfold4: 0.635 Sensitivity UNAFold: 0.766 Vsfold4: 0.625 Positive Predictive Value UNAFold: 0.747 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.712 Murlet(seed): 0.594 Sensitivity UNAFold: 0.716 Murlet(seed): 0.418 Positive Predictive Value UNAFold: 0.717 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.763 MCFold: 0.622 Sensitivity UNAFold: 0.777 MCFold: 0.663 Positive Predictive Value UNAFold: 0.758 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.745 Vsfold5: 0.593 Sensitivity UNAFold: 0.758 Vsfold5: 0.595 Positive Predictive Value UNAFold: 0.738 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.582 RNAwolf: 0.436 Sensitivity UNAFold: 0.608 RNAwolf: 0.446 Positive Predictive Value UNAFold: 0.559 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.674 CMfinder(20): 0.652 Sensitivity UNAFold: 0.684 CMfinder(20): 0.518 Positive Predictive Value UNAFold: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.658 NanoFolder: 0.394 Sensitivity UNAFold: 0.673 NanoFolder: 0.485 Positive Predictive Value UNAFold: 0.651 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.815 RDfolder: 0.677 Sensitivity UNAFold: 0.812 RDfolder: 0.637 Positive Predictive Value UNAFold: 0.827 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.649 RSpredict(seed): 0.449 Sensitivity UNAFold: 0.670 RSpredict(seed): 0.304 Positive Predictive Value UNAFold: 0.631 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.649 UNAFold: 0.578 Sensitivity Multilign(seed): 0.591 UNAFold: 0.577 Positive Predictive Value Multilign(seed): 0.724 UNAFold: 0.591 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.589 PPfold(seed): 0.094 Sensitivity UNAFold: 0.595 PPfold(seed): 0.019 Positive Predictive Value UNAFold: 0.593 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.678 Carnac(seed): 0.474 Sensitivity UNAFold: 0.686 Carnac(seed): 0.239 Positive Predictive Value UNAFold: 0.672 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.683 Mastr(seed): 0.279 Sensitivity UNAFold: 0.702 Mastr(seed): 0.088 Positive Predictive Value UNAFold: 0.671 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs PETfold_2.0(seed) Matthews Correlation Coefficient UNAFold: 0.868 PETfold_2.0(seed): 0.866 Sensitivity UNAFold: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value UNAFold: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 UNAFold: 0.752 Sensitivity PETfold_2.0(20): 0.889 UNAFold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 UNAFold: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
ProbKnot	31 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.793 ProbKnot: 0.653 Sensitivity CentroidAlifold(20): 0.704 ProbKnot: 0.681 Positive Predictive Value CentroidAlifold(20): 0.898 ProbKnot: 0.632 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 ProbKnot: 0.622 Sensitivity PETfold_pre2.0(seed): 0.841 ProbKnot: 0.637 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	49 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.680 ProbKnot: 0.569 Sensitivity ContextFold: 0.671 ProbKnot: 0.594 Positive Predictive Value ContextFold: 0.689 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.769 ProbKnot: 0.648 Sensitivity MXScarna(seed): 0.733 ProbKnot: 0.671 Positive Predictive Value MXScarna(seed): 0.807 ProbKnot: 0.627 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.762 ProbKnot: 0.679 Sensitivity RNAalifold(20): 0.669 ProbKnot: 0.700 Positive Predictive Value RNAalifold(20): 0.872 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	18 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 ProbKnot: 0.596 Sensitivity PETfold_pre2.0(20): 0.776 ProbKnot: 0.627 Positive Predictive Value PETfold_pre2.0(20): 0.815 ProbKnot: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.812 ProbKnot: 0.670 Sensitivity PPfold(20): 0.753 ProbKnot: 0.686 Positive Predictive Value PPfold(20): 0.880 ProbKnot: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.06761512825e-08	57 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.675 ProbKnot: 0.579 Sensitivity IPknot: 0.645 ProbKnot: 0.604 Positive Predictive Value IPknot: 0.707 ProbKnot: 0.557 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.736 ProbKnot: 0.679 Sensitivity MXScarna(20): 0.697 ProbKnot: 0.700 Positive Predictive Value MXScarna(20): 0.782 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.721 ProbKnot: 0.679 Sensitivity RNASampler(20): 0.625 ProbKnot: 0.700 Positive Predictive Value RNASampler(20): 0.837 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.773 ProbKnot: 0.670 Sensitivity TurboFold(20): 0.737 ProbKnot: 0.686 Positive Predictive Value TurboFold(20): 0.817 ProbKnot: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	44 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 ProbKnot: 0.647 Sensitivity CentroidAlifold(seed): 0.610 ProbKnot: 0.673 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.624 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.668 ProbKnot: 0.635 Sensitivity CentroidFold: 0.659 ProbKnot: 0.665 Positive Predictive Value CentroidFold: 0.679 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.659 ProbKnot: 0.638 Sensitivity Sfold: 0.663 ProbKnot: 0.668 Positive Predictive Value Sfold: 0.656 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 ProbKnot: 0.668 Sensitivity CentroidHomfold‑LAST: 0.629 ProbKnot: 0.695 Positive Predictive Value CentroidHomfold‑LAST: 0.803 ProbKnot: 0.650 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.652 ProbKnot: 0.638 Sensitivity Contrafold: 0.671 ProbKnot: 0.668 Positive Predictive Value Contrafold: 0.634 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 7.5939721025e-08	23 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.713 ProbKnot: 0.600 Sensitivity RNAalifold(seed): 0.593 ProbKnot: 0.624 Positive Predictive Value RNAalifold(seed): 0.860 ProbKnot: 0.579 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	93 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.643 ProbKnot: 0.638 Sensitivity MaxExpect: 0.663 ProbKnot: 0.668 Positive Predictive Value MaxExpect: 0.626 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.711 ProbKnot: 0.698 Sensitivity HotKnots: 0.742 ProbKnot: 0.732 Positive Predictive Value HotKnots: 0.686 ProbKnot: 0.670 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 2.45033651981e-07	93 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.638 UNAFold: 0.636 Sensitivity ProbKnot: 0.668 UNAFold: 0.661 Positive Predictive Value ProbKnot: 0.612 UNAFold: 0.613 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 0.00586086047676		+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.679 Murlet(20): 0.667 Sensitivity ProbKnot: 0.700 Murlet(20): 0.567 Positive Predictive Value ProbKnot: 0.664 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.6410608252e-08	- PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.648 ProbKnot: 0.643 Sensitivity PknotsRG: 0.683 ProbKnot: 0.678 Positive Predictive Value PknotsRG: 0.616 ProbKnot: 0.613 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.00031545328565	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.638 RNAfold: 0.633 Sensitivity ProbKnot: 0.668 RNAfold: 0.662 Positive Predictive Value ProbKnot: 0.612 RNAfold: 0.607 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 1.41488137601e-05	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.698 RNAshapes: 0.691 Sensitivity ProbKnot: 0.732 RNAshapes: 0.714 Positive Predictive Value ProbKnot: 0.670 RNAshapes: 0.675 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 4.87628608759e-06	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.638 Fold: 0.619 Sensitivity ProbKnot: 0.668 Fold: 0.652 Positive Predictive Value ProbKnot: 0.612 Fold: 0.590 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 4.1569883686e-08	- TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.647 ProbKnot: 0.590 Sensitivity TurboFold(seed): 0.615 ProbKnot: 0.607 Positive Predictive Value TurboFold(seed): 0.691 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.626 Afold: 0.604 Sensitivity ProbKnot: 0.665 Afold: 0.644 Positive Predictive Value ProbKnot: 0.592 Afold: 0.568 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.679 Carnac(20): 0.646 Sensitivity ProbKnot: 0.700 Carnac(20): 0.470 Positive Predictive Value ProbKnot: 0.664 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.650 RSpredict(20): 0.631 Sensitivity ProbKnot: 0.677 RSpredict(20): 0.569 Positive Predictive Value ProbKnot: 0.631 RSpredict(20): 0.706 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.698 RNAsubopt: 0.689 Sensitivity ProbKnot: 0.732 RNAsubopt: 0.722 Positive Predictive Value ProbKnot: 0.670 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 1.27481660653e-07	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.743 Cylofold: 0.698 Sensitivity ProbKnot: 0.766 Cylofold: 0.683 Positive Predictive Value ProbKnot: 0.730 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.636 McQFold: 0.567 Sensitivity ProbKnot: 0.666 McQFold: 0.581 Positive Predictive Value ProbKnot: 0.610 McQFold: 0.556 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.633 RNASLOpt: 0.580 Sensitivity ProbKnot: 0.662 RNASLOpt: 0.559 Positive Predictive Value ProbKnot: 0.612 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.761 Pknots: 0.695 Sensitivity ProbKnot: 0.782 Pknots: 0.719 Positive Predictive Value ProbKnot: 0.747 Pknots: 0.681 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.683 ProbKnot: 0.667 Sensitivity CRWrnafold: 0.690 ProbKnot: 0.692 Positive Predictive Value CRWrnafold: 0.689 ProbKnot: 0.654 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.27481660653e-07	- Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.652 ProbKnot: 0.646 Sensitivity Multilign(20): 0.624 ProbKnot: 0.659 Positive Predictive Value Multilign(20): 0.692 ProbKnot: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.0194307659e-06	+ ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.650 RNASampler(seed): 0.604 Sensitivity ProbKnot: 0.700 RNASampler(seed): 0.496 Positive Predictive Value ProbKnot: 0.611 RNASampler(seed): 0.744 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.05332335737e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.819 Alterna: 0.781 Sensitivity ProbKnot: 0.847 Alterna: 0.798 Positive Predictive Value ProbKnot: 0.801 Alterna: 0.776 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.679 Mastr(20): 0.573 Sensitivity ProbKnot: 0.700 Mastr(20): 0.412 Positive Predictive Value ProbKnot: 0.664 Mastr(20): 0.804 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.727 Vsfold4: 0.607 Sensitivity ProbKnot: 0.758 Vsfold4: 0.600 Positive Predictive Value ProbKnot: 0.703 Vsfold4: 0.622 Number of pairs reference - predicted secondary structure: 85 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.633 Murlet(seed): 0.544 Sensitivity ProbKnot: 0.653 Murlet(seed): 0.362 Positive Predictive Value ProbKnot: 0.622 Murlet(seed): 0.829 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.726 MCFold: 0.604 Sensitivity ProbKnot: 0.753 MCFold: 0.640 Positive Predictive Value ProbKnot: 0.708 MCFold: 0.581 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.715 Vsfold5: 0.565 Sensitivity ProbKnot: 0.746 Vsfold5: 0.570 Positive Predictive Value ProbKnot: 0.691 Vsfold5: 0.570 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.582 RNAwolf: 0.436 Sensitivity ProbKnot: 0.609 RNAwolf: 0.446 Positive Predictive Value ProbKnot: 0.559 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.687 CMfinder(20): 0.652 Sensitivity ProbKnot: 0.675 CMfinder(20): 0.518 Positive Predictive Value ProbKnot: 0.706 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.694 NanoFolder: 0.394 Sensitivity ProbKnot: 0.723 NanoFolder: 0.485 Positive Predictive Value ProbKnot: 0.673 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.801 RDfolder: 0.675 Sensitivity ProbKnot: 0.823 RDfolder: 0.639 Positive Predictive Value ProbKnot: 0.791 RDfolder: 0.729 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.646 RSpredict(seed): 0.425 Sensitivity ProbKnot: 0.671 RSpredict(seed): 0.286 Positive Predictive Value ProbKnot: 0.623 RSpredict(seed): 0.634 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.654 Multilign(seed): 0.649 Sensitivity ProbKnot: 0.649 Multilign(seed): 0.591 Positive Predictive Value ProbKnot: 0.668 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.641 PPfold(seed): 0.094 Sensitivity ProbKnot: 0.655 PPfold(seed): 0.019 Positive Predictive Value ProbKnot: 0.638 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.651 Carnac(seed): 0.486 Sensitivity ProbKnot: 0.663 Carnac(seed): 0.253 Positive Predictive Value ProbKnot: 0.640 Carnac(seed): 0.934 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.663 Mastr(seed): 0.221 Sensitivity ProbKnot: 0.696 Mastr(seed): 0.049 Positive Predictive Value ProbKnot: 0.638 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 ProbKnot: 0.848 Sensitivity PETfold_2.0(seed): 0.845 ProbKnot: 0.879 Positive Predictive Value PETfold_2.0(seed): 0.891 ProbKnot: 0.823 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.905 ProbKnot: 0.723 Sensitivity PETfold_2.0(20): 0.889 ProbKnot: 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 ProbKnot: 0.677 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Murlet(20)	39 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Murlet(20): 0.702 Sensitivity CentroidAlifold(20): 0.728 Murlet(20): 0.610 Positive Predictive Value CentroidAlifold(20): 0.901 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Murlet(20): 0.682 Sensitivity PETfold_pre2.0(seed): 0.858 Murlet(20): 0.611 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.48055519165e-08	11 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.781 Murlet(20): 0.625 Sensitivity ContextFold: 0.731 Murlet(20): 0.548 Positive Predictive Value ContextFold: 0.840 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	33 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Murlet(20): 0.688 Sensitivity MXScarna(seed): 0.732 Murlet(20): 0.589 Positive Predictive Value MXScarna(seed): 0.825 Murlet(20): 0.810 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Murlet(20): 0.693 Sensitivity RNAalifold(20): 0.704 Murlet(20): 0.594 Positive Predictive Value RNAalifold(20): 0.891 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Murlet(20): 0.682 Sensitivity PETfold_pre2.0(20): 0.776 Murlet(20): 0.611 Positive Predictive Value PETfold_pre2.0(20): 0.815 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.812 Murlet(20): 0.663 Sensitivity PPfold(20): 0.753 Murlet(20): 0.593 Positive Predictive Value PPfold(20): 0.880 Murlet(20): 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	14 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.712 Murlet(20): 0.671 Sensitivity IPknot: 0.678 Murlet(20): 0.598 Positive Predictive Value IPknot: 0.756 Murlet(20): 0.761 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	34 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Murlet(20): 0.693 Sensitivity MXScarna(20): 0.720 Murlet(20): 0.594 Positive Predictive Value MXScarna(20): 0.796 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Murlet(20): 0.693 Sensitivity RNASampler(20): 0.663 Murlet(20): 0.594 Positive Predictive Value RNASampler(20): 0.856 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.773 Murlet(20): 0.663 Sensitivity TurboFold(20): 0.737 Murlet(20): 0.593 Positive Predictive Value TurboFold(20): 0.817 Murlet(20): 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	39 Murlet(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Murlet(20): 0.702 CentroidAlifold(seed): 0.695 Sensitivity Murlet(20): 0.610 CentroidAlifold(seed): 0.528 Positive Predictive Value Murlet(20): 0.814 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.0144324399527	39 Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.702 CentroidFold: 0.690 Sensitivity Murlet(20): 0.610 CentroidFold: 0.689 Positive Predictive Value Murlet(20): 0.814 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 2.12176083234e-07	34 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.707 Murlet(20): 0.693 Sensitivity Sfold: 0.683 Murlet(20): 0.594 Positive Predictive Value Sfold: 0.736 Murlet(20): 0.815 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.37177523642e-07	14 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Murlet(20): 0.684 Sensitivity CentroidHomfold‑LAST: 0.744 Murlet(20): 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.87872347734e-08	34 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.693 Contrafold: 0.664 Sensitivity Murlet(20): 0.594 Contrafold: 0.681 Positive Predictive Value Murlet(20): 0.815 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Murlet(20): 0.595 Sensitivity RNAalifold(seed): 0.488 Murlet(20): 0.477 Positive Predictive Value RNAalifold(seed): 0.931 Murlet(20): 0.749 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	32 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.690 Murlet(20): 0.688 Sensitivity MaxExpect: 0.693 Murlet(20): 0.590 Positive Predictive Value MaxExpect: 0.694 Murlet(20): 0.809 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0186613811547	34 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.693 HotKnots: 0.668 Sensitivity Murlet(20): 0.594 HotKnots: 0.692 Positive Predictive Value Murlet(20): 0.815 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.59499054376e-07	34 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.693 UNAFold: 0.692 Sensitivity Murlet(20): 0.594 UNAFold: 0.701 Positive Predictive Value Murlet(20): 0.815 UNAFold: 0.689 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.183291550418	24 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.679 Murlet(20): 0.667 Sensitivity ProbKnot: 0.700 Murlet(20): 0.567 Positive Predictive Value ProbKnot: 0.664 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.6410608252e-08		= Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.693 PknotsRG: 0.687 Sensitivity Murlet(20): 0.594 PknotsRG: 0.709 Positive Predictive Value Murlet(20): 0.815 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0280322430983	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.693 RNAfold: 0.677 Sensitivity Murlet(20): 0.594 RNAfold: 0.694 Positive Predictive Value Murlet(20): 0.815 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.14125540109e-07	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.693 RNAshapes: 0.685 Sensitivity Murlet(20): 0.594 RNAshapes: 0.694 Positive Predictive Value Murlet(20): 0.815 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.17043408065e-05	- Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.694 Murlet(20): 0.667 Sensitivity Fold: 0.715 Murlet(20): 0.567 Positive Predictive Value Fold: 0.680 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 Murlet(20): 0.621 Sensitivity TurboFold(seed): 0.653 Murlet(20): 0.546 Positive Predictive Value TurboFold(seed): 0.723 Murlet(20): 0.715 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.677 Afold: 0.639 Sensitivity Murlet(20): 0.571 Afold: 0.658 Positive Predictive Value Murlet(20): 0.807 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.0871064633e-07	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.693 Carnac(20): 0.686 Sensitivity Murlet(20): 0.594 Carnac(20): 0.518 Positive Predictive Value Murlet(20): 0.815 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.57295429596e-06	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.697 RSpredict(20): 0.660 Sensitivity Murlet(20): 0.604 RSpredict(20): 0.597 Positive Predictive Value Murlet(20): 0.810 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.693 RNAsubopt: 0.660 Sensitivity Murlet(20): 0.594 RNAsubopt: 0.684 Positive Predictive Value Murlet(20): 0.815 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.739 Cylofold: 0.715 Sensitivity Murlet(20): 0.645 Cylofold: 0.713 Positive Predictive Value Murlet(20): 0.854 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 7.36344111049e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.693 McQFold: 0.641 Sensitivity Murlet(20): 0.594 McQFold: 0.648 Positive Predictive Value Murlet(20): 0.815 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Murlet(20): 0.625 Sensitivity RNASLOpt: 0.616 Murlet(20): 0.548 Positive Predictive Value RNASLOpt: 0.662 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00207278670317	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.716 Pknots: 0.619 Sensitivity Murlet(20): 0.625 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.827 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.677 CRWrnafold: 0.668 Sensitivity Murlet(20): 0.604 CRWrnafold: 0.683 Positive Predictive Value Murlet(20): 0.767 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.664 Multilign(20): 0.652 Sensitivity Murlet(20): 0.573 Multilign(20): 0.624 Positive Predictive Value Murlet(20): 0.779 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.61878218056e-06	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Murlet(20): 0.585 Sensitivity RNASampler(seed): 0.604 Murlet(20): 0.540 Positive Predictive Value RNASampler(seed): 0.748 Murlet(20): 0.639 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.671 Sensitivity Murlet(20): 0.695 Alterna: 0.680 Positive Predictive Value Murlet(20): 0.882 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.693 Mastr(20): 0.620 Sensitivity Murlet(20): 0.594 Mastr(20): 0.473 Positive Predictive Value Murlet(20): 0.815 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.703 Vsfold4: 0.561 Sensitivity Murlet(20): 0.601 Vsfold4: 0.556 Positive Predictive Value Murlet(20): 0.827 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.620 Murlet(seed): 0.557 Sensitivity Murlet(20): 0.509 Murlet(seed): 0.355 Positive Predictive Value Murlet(20): 0.763 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.717 MCFold: 0.499 Sensitivity Murlet(20): 0.639 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.810 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.703 Vsfold5: 0.494 Sensitivity Murlet(20): 0.601 Vsfold5: 0.496 Positive Predictive Value Murlet(20): 0.827 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.705 RNAwolf: 0.438 Sensitivity Murlet(20): 0.637 RNAwolf: 0.454 Positive Predictive Value Murlet(20): 0.786 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.696 CMfinder(20): 0.652 Sensitivity Murlet(20): 0.632 CMfinder(20): 0.518 Positive Predictive Value Murlet(20): 0.774 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.714 NanoFolder: 0.329 Sensitivity Murlet(20): 0.637 NanoFolder: 0.405 Positive Predictive Value Murlet(20): 0.807 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.759 RDfolder: 0.636 Sensitivity Murlet(20): 0.661 RDfolder: 0.602 Positive Predictive Value Murlet(20): 0.882 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.697 RSpredict(seed): 0.230 Sensitivity Murlet(20): 0.604 RSpredict(seed): 0.114 Positive Predictive Value Murlet(20): 0.810 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Murlet(20): 0.698 Sensitivity Multilign(seed): 0.682 Murlet(20): 0.636 Positive Predictive Value Multilign(seed): 0.793 Murlet(20): 0.774 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.671 PPfold(seed): 0.046 Sensitivity Murlet(20): 0.598 PPfold(seed): 0.009 Positive Predictive Value Murlet(20): 0.761 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.671 Carnac(seed): 0.220 Sensitivity Murlet(20): 0.566 Carnac(seed): 0.049 Positive Predictive Value Murlet(20): 0.802 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.693 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.594 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.815 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Murlet(20): 0.881 Sensitivity PETfold_2.0(seed): 0.889 Murlet(20): 0.778 Positive Predictive Value PETfold_2.0(seed): 0.923 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Murlet(20): 0.881 Sensitivity PETfold_2.0(20): 0.889 Murlet(20): 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PknotsRG	39 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.808 PknotsRG: 0.670 Sensitivity CentroidAlifold(20): 0.728 PknotsRG: 0.700 Positive Predictive Value CentroidAlifold(20): 0.901 PknotsRG: 0.648 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 PknotsRG: 0.668 Sensitivity PETfold_pre2.0(seed): 0.826 PknotsRG: 0.701 Positive Predictive Value PETfold_pre2.0(seed): 0.913 PknotsRG: 0.644 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.612 PknotsRG: 0.573 Sensitivity ContextFold: 0.604 PknotsRG: 0.608 Positive Predictive Value ContextFold: 0.622 PknotsRG: 0.541 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.769 PknotsRG: 0.691 Sensitivity MXScarna(seed): 0.727 PknotsRG: 0.717 Positive Predictive Value MXScarna(seed): 0.819 PknotsRG: 0.671 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.790 PknotsRG: 0.687 Sensitivity RNAalifold(20): 0.704 PknotsRG: 0.709 Positive Predictive Value RNAalifold(20): 0.891 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 PknotsRG: 0.641 Sensitivity PETfold_pre2.0(20): 0.776 PknotsRG: 0.689 Positive Predictive Value PETfold_pre2.0(20): 0.815 PknotsRG: 0.604 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.33194562506e-08	15 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.812 PknotsRG: 0.696 Sensitivity PPfold(20): 0.753 PknotsRG: 0.718 Positive Predictive Value PPfold(20): 0.880 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	56 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.652 PknotsRG: 0.588 Sensitivity IPknot: 0.617 PknotsRG: 0.623 Positive Predictive Value IPknot: 0.691 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.755 PknotsRG: 0.687 Sensitivity MXScarna(20): 0.720 PknotsRG: 0.709 Positive Predictive Value MXScarna(20): 0.796 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.751 PknotsRG: 0.687 Sensitivity RNASampler(20): 0.663 PknotsRG: 0.709 Positive Predictive Value RNASampler(20): 0.856 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.773 PknotsRG: 0.696 Sensitivity TurboFold(20): 0.737 PknotsRG: 0.718 Positive Predictive Value TurboFold(20): 0.817 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	60 PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.690 CentroidAlifold(seed): 0.686 Sensitivity PknotsRG: 0.722 CentroidAlifold(seed): 0.535 Positive Predictive Value PknotsRG: 0.665 CentroidAlifold(seed): 0.884 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 0.211284698433	136 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.664 PknotsRG: 0.592 Sensitivity CentroidFold: 0.658 PknotsRG: 0.635 Positive Predictive Value CentroidFold: 0.672 PknotsRG: 0.552 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.616 PknotsRG: 0.575 Sensitivity Sfold: 0.617 PknotsRG: 0.613 Positive Predictive Value Sfold: 0.616 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 PknotsRG: 0.697 Sensitivity CentroidHomfold‑LAST: 0.629 PknotsRG: 0.718 Positive Predictive Value CentroidHomfold‑LAST: 0.803 PknotsRG: 0.683 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 5.3419901105e-07	139 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.658 PknotsRG: 0.575 Sensitivity Contrafold: 0.681 PknotsRG: 0.613 Positive Predictive Value Contrafold: 0.636 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.680 PknotsRG: 0.677 Sensitivity RNAalifold(seed): 0.525 PknotsRG: 0.711 Positive Predictive Value RNAalifold(seed): 0.885 PknotsRG: 0.650 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.935722063919	117 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.670 PknotsRG: 0.616 Sensitivity MaxExpect: 0.685 PknotsRG: 0.646 Positive Predictive Value MaxExpect: 0.656 PknotsRG: 0.589 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.737 PknotsRG: 0.718 Sensitivity HotKnots: 0.761 PknotsRG: 0.744 Positive Predictive Value HotKnots: 0.719 PknotsRG: 0.698 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.591 PknotsRG: 0.575 Sensitivity UNAFold: 0.623 PknotsRG: 0.613 Positive Predictive Value UNAFold: 0.561 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.648 ProbKnot: 0.643 Sensitivity PknotsRG: 0.683 ProbKnot: 0.678 Positive Predictive Value PknotsRG: 0.616 ProbKnot: 0.613 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.00031545328565	34 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.693 PknotsRG: 0.687 Sensitivity Murlet(20): 0.594 PknotsRG: 0.709 Positive Predictive Value Murlet(20): 0.815 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.0280322430983		- RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.585 PknotsRG: 0.575 Sensitivity RNAfold: 0.622 PknotsRG: 0.613 Positive Predictive Value RNAfold: 0.550 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	= PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.718 RNAshapes: 0.714 Sensitivity PknotsRG: 0.744 RNAshapes: 0.731 Positive Predictive Value PknotsRG: 0.698 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00181847574797	+ PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.657 Fold: 0.650 Sensitivity PknotsRG: 0.691 Fold: 0.683 Positive Predictive Value PknotsRG: 0.627 Fold: 0.621 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 7.33397498022e-05	+ PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.662 TurboFold(seed): 0.647 Sensitivity PknotsRG: 0.683 TurboFold(seed): 0.615 Positive Predictive Value PknotsRG: 0.651 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39027542218e-05	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.564 PknotsRG: 0.551 Sensitivity Afold: 0.605 PknotsRG: 0.593 Positive Predictive Value Afold: 0.526 PknotsRG: 0.513 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	= PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.687 Carnac(20): 0.686 Sensitivity PknotsRG: 0.709 Carnac(20): 0.518 Positive Predictive Value PknotsRG: 0.673 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.903713469855	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.671 RSpredict(20): 0.660 Sensitivity PknotsRG: 0.702 RSpredict(20): 0.597 Positive Predictive Value PknotsRG: 0.648 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 1.34568509467e-07	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.718 RNAsubopt: 0.703 Sensitivity PknotsRG: 0.744 RNAsubopt: 0.730 Positive Predictive Value PknotsRG: 0.698 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.743 Cylofold: 0.701 Sensitivity PknotsRG: 0.757 Cylofold: 0.686 Positive Predictive Value PknotsRG: 0.738 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.573 McQFold: 0.496 Sensitivity PknotsRG: 0.612 McQFold: 0.477 Positive Predictive Value PknotsRG: 0.538 McQFold: 0.517 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.653 RNASLOpt: 0.580 Sensitivity PknotsRG: 0.684 RNASLOpt: 0.559 Positive Predictive Value PknotsRG: 0.630 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.758 Pknots: 0.705 Sensitivity PknotsRG: 0.774 Pknots: 0.732 Positive Predictive Value PknotsRG: 0.750 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.720 CRWrnafold: 0.683 Sensitivity PknotsRG: 0.743 CRWrnafold: 0.690 Positive Predictive Value PknotsRG: 0.708 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.701 Multilign(20): 0.652 Sensitivity PknotsRG: 0.712 Multilign(20): 0.624 Positive Predictive Value PknotsRG: 0.699 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.741 RNASampler(seed): 0.728 Sensitivity PknotsRG: 0.771 RNASampler(seed): 0.634 Positive Predictive Value PknotsRG: 0.719 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.30881340954e-06	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.803 Alterna: 0.767 Sensitivity PknotsRG: 0.808 Alterna: 0.777 Positive Predictive Value PknotsRG: 0.808 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.687 Mastr(20): 0.620 Sensitivity PknotsRG: 0.709 Mastr(20): 0.473 Positive Predictive Value PknotsRG: 0.673 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.735 Vsfold4: 0.635 Sensitivity PknotsRG: 0.757 Vsfold4: 0.625 Positive Predictive Value PknotsRG: 0.720 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.735 Murlet(seed): 0.594 Sensitivity PknotsRG: 0.747 Murlet(seed): 0.418 Positive Predictive Value PknotsRG: 0.730 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.757 MCFold: 0.622 Sensitivity PknotsRG: 0.781 MCFold: 0.663 Positive Predictive Value PknotsRG: 0.742 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.732 Vsfold5: 0.593 Sensitivity PknotsRG: 0.754 Vsfold5: 0.595 Positive Predictive Value PknotsRG: 0.717 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.607 RNAwolf: 0.407 Sensitivity PknotsRG: 0.644 RNAwolf: 0.419 Positive Predictive Value PknotsRG: 0.574 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.674 CMfinder(20): 0.652 Sensitivity PknotsRG: 0.684 CMfinder(20): 0.518 Positive Predictive Value PknotsRG: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.701 NanoFolder: 0.394 Sensitivity PknotsRG: 0.725 NanoFolder: 0.485 Positive Predictive Value PknotsRG: 0.685 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.800 RDfolder: 0.677 Sensitivity PknotsRG: 0.806 RDfolder: 0.637 Positive Predictive Value PknotsRG: 0.804 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.691 RSpredict(seed): 0.316 Sensitivity PknotsRG: 0.723 RSpredict(seed): 0.179 Positive Predictive Value PknotsRG: 0.666 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.649 PknotsRG: 0.645 Sensitivity Multilign(seed): 0.591 PknotsRG: 0.644 Positive Predictive Value Multilign(seed): 0.724 PknotsRG: 0.657 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.674 PPfold(seed): 0.094 Sensitivity PknotsRG: 0.685 PPfold(seed): 0.019 Positive Predictive Value PknotsRG: 0.672 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.740 Carnac(seed): 0.277 Sensitivity PknotsRG: 0.753 Carnac(seed): 0.078 Positive Predictive Value PknotsRG: 0.734 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.693 Mastr(seed): 0.279 Sensitivity PknotsRG: 0.720 Mastr(seed): 0.088 Positive Predictive Value PknotsRG: 0.674 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs PETfold_2.0(seed) Matthews Correlation Coefficient PknotsRG: 0.868 PETfold_2.0(seed): 0.866 Sensitivity PknotsRG: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value PknotsRG: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.905 PknotsRG: 0.752 Sensitivity PETfold_2.0(20): 0.889 PknotsRG: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 PknotsRG: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAfold	39 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAfold: 0.654 Sensitivity CentroidAlifold(20): 0.728 RNAfold: 0.680 Positive Predictive Value CentroidAlifold(20): 0.901 RNAfold: 0.636 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 RNAfold: 0.606 Sensitivity PETfold_pre2.0(seed): 0.841 RNAfold: 0.625 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAfold: 0.589 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	49 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.680 RNAfold: 0.566 Sensitivity ContextFold: 0.671 RNAfold: 0.592 Positive Predictive Value ContextFold: 0.689 RNAfold: 0.542 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.786 RNAfold: 0.661 Sensitivity MXScarna(seed): 0.749 RNAfold: 0.682 Positive Predictive Value MXScarna(seed): 0.825 RNAfold: 0.642 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAfold: 0.677 Sensitivity RNAalifold(20): 0.704 RNAfold: 0.694 Positive Predictive Value RNAalifold(20): 0.891 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAfold: 0.600 Sensitivity PETfold_pre2.0(20): 0.776 RNAfold: 0.636 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAfold: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	15 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.812 RNAfold: 0.674 Sensitivity PPfold(20): 0.753 RNAfold: 0.686 Positive Predictive Value PPfold(20): 0.880 RNAfold: 0.671 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	57 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.675 RNAfold: 0.578 Sensitivity IPknot: 0.645 RNAfold: 0.604 Positive Predictive Value IPknot: 0.707 RNAfold: 0.555 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.755 RNAfold: 0.677 Sensitivity MXScarna(20): 0.720 RNAfold: 0.694 Positive Predictive Value MXScarna(20): 0.796 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.751 RNAfold: 0.677 Sensitivity RNASampler(20): 0.663 RNAfold: 0.694 Positive Predictive Value RNASampler(20): 0.856 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.773 RNAfold: 0.674 Sensitivity TurboFold(20): 0.737 RNAfold: 0.686 Positive Predictive Value TurboFold(20): 0.817 RNAfold: 0.671 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	61 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RNAfold: 0.658 Sensitivity CentroidAlifold(seed): 0.602 RNAfold: 0.682 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAfold: 0.638 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.667 RNAfold: 0.593 Sensitivity CentroidFold: 0.661 RNAfold: 0.633 Positive Predictive Value CentroidFold: 0.675 RNAfold: 0.557 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.613 RNAfold: 0.583 Sensitivity Sfold: 0.614 RNAfold: 0.619 Positive Predictive Value Sfold: 0.612 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAfold: 0.702 Sensitivity CentroidHomfold‑LAST: 0.629 RNAfold: 0.713 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAfold: 0.696 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 0.0200535500971	140 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.662 RNAfold: 0.583 Sensitivity Contrafold: 0.684 RNAfold: 0.619 Positive Predictive Value Contrafold: 0.640 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.740 RNAfold: 0.639 Sensitivity RNAalifold(seed): 0.624 RNAfold: 0.664 Positive Predictive Value RNAalifold(seed): 0.879 RNAfold: 0.617 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.663 RNAfold: 0.621 Sensitivity MaxExpect: 0.679 RNAfold: 0.647 Positive Predictive Value MaxExpect: 0.648 RNAfold: 0.597 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.737 RNAfold: 0.726 Sensitivity HotKnots: 0.761 RNAfold: 0.747 Positive Predictive Value HotKnots: 0.719 RNAfold: 0.711 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.589 RNAfold: 0.583 Sensitivity UNAFold: 0.620 RNAfold: 0.619 Positive Predictive Value UNAFold: 0.560 RNAfold: 0.550 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.638 RNAfold: 0.633 Sensitivity ProbKnot: 0.668 RNAfold: 0.662 Positive Predictive Value ProbKnot: 0.612 RNAfold: 0.607 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 1.41488137601e-05	34 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.693 RNAfold: 0.677 Sensitivity Murlet(20): 0.594 RNAfold: 0.694 Positive Predictive Value Murlet(20): 0.815 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.14125540109e-07	139 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.585 PknotsRG: 0.575 Sensitivity RNAfold: 0.622 PknotsRG: 0.613 Positive Predictive Value RNAfold: 0.550 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.726 RNAshapes: 0.714 Sensitivity RNAfold: 0.747 RNAshapes: 0.731 Positive Predictive Value RNAfold: 0.711 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.645 Fold: 0.636 Sensitivity RNAfold: 0.673 Fold: 0.668 Positive Predictive Value RNAfold: 0.620 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 9.291770879e-07	- TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAfold: 0.629 Sensitivity TurboFold(seed): 0.615 RNAfold: 0.637 Positive Predictive Value TurboFold(seed): 0.691 RNAfold: 0.630 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.56154924607e-07	- Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.564 RNAfold: 0.562 Sensitivity Afold: 0.605 RNAfold: 0.603 Positive Predictive Value Afold: 0.526 RNAfold: 0.524 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 5.84585956207e-05	- Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.686 RNAfold: 0.677 Sensitivity Carnac(20): 0.518 RNAfold: 0.694 Positive Predictive Value Carnac(20): 0.915 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.16217446969e-05	- RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.660 RNAfold: 0.655 Sensitivity RSpredict(20): 0.597 RNAfold: 0.681 Positive Predictive Value RSpredict(20): 0.735 RNAfold: 0.636 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000102525955954	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.726 RNAsubopt: 0.703 Sensitivity RNAfold: 0.747 RNAsubopt: 0.730 Positive Predictive Value RNAfold: 0.711 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.738 Cylofold: 0.701 Sensitivity RNAfold: 0.746 Cylofold: 0.686 Positive Predictive Value RNAfold: 0.738 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.582 McQFold: 0.501 Sensitivity RNAfold: 0.618 McQFold: 0.483 Positive Predictive Value RNAfold: 0.549 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.652 RNASLOpt: 0.580 Sensitivity RNAfold: 0.672 RNASLOpt: 0.559 Positive Predictive Value RNAfold: 0.638 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.766 Pknots: 0.705 Sensitivity RNAfold: 0.776 Pknots: 0.732 Positive Predictive Value RNAfold: 0.763 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.706 CRWrnafold: 0.683 Sensitivity RNAfold: 0.715 CRWrnafold: 0.690 Positive Predictive Value RNAfold: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.679 Multilign(20): 0.652 Sensitivity RNAfold: 0.680 Multilign(20): 0.624 Positive Predictive Value RNAfold: 0.687 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.763 RNASampler(seed): 0.728 Sensitivity RNAfold: 0.794 RNASampler(seed): 0.634 Positive Predictive Value RNAfold: 0.739 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.817 Alterna: 0.767 Sensitivity RNAfold: 0.820 Alterna: 0.777 Positive Predictive Value RNAfold: 0.824 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.677 Mastr(20): 0.620 Sensitivity RNAfold: 0.694 Mastr(20): 0.473 Positive Predictive Value RNAfold: 0.667 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.742 Vsfold4: 0.635 Sensitivity RNAfold: 0.760 Vsfold4: 0.625 Positive Predictive Value RNAfold: 0.732 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.732 Murlet(seed): 0.594 Sensitivity RNAfold: 0.740 Murlet(seed): 0.418 Positive Predictive Value RNAfold: 0.732 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.758 MCFold: 0.622 Sensitivity RNAfold: 0.775 MCFold: 0.663 Positive Predictive Value RNAfold: 0.749 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.737 Vsfold5: 0.593 Sensitivity RNAfold: 0.754 Vsfold5: 0.595 Positive Predictive Value RNAfold: 0.726 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.587 RNAwolf: 0.436 Sensitivity RNAfold: 0.614 RNAwolf: 0.446 Positive Predictive Value RNAfold: 0.562 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.674 CMfinder(20): 0.652 Sensitivity RNAfold: 0.684 CMfinder(20): 0.518 Positive Predictive Value RNAfold: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.703 NanoFolder: 0.394 Sensitivity RNAfold: 0.717 NanoFolder: 0.485 Positive Predictive Value RNAfold: 0.696 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.802 RDfolder: 0.677 Sensitivity RNAfold: 0.803 RDfolder: 0.637 Positive Predictive Value RNAfold: 0.810 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.659 RSpredict(seed): 0.449 Sensitivity RNAfold: 0.683 RSpredict(seed): 0.304 Positive Predictive Value RNAfold: 0.638 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.649 RNAfold: 0.642 Sensitivity Multilign(seed): 0.591 RNAfold: 0.644 Positive Predictive Value Multilign(seed): 0.724 RNAfold: 0.650 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.653 PPfold(seed): 0.094 Sensitivity RNAfold: 0.657 PPfold(seed): 0.019 Positive Predictive Value RNAfold: 0.657 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.680 Carnac(seed): 0.474 Sensitivity RNAfold: 0.691 Carnac(seed): 0.239 Positive Predictive Value RNAfold: 0.671 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.693 Mastr(seed): 0.279 Sensitivity RNAfold: 0.716 Mastr(seed): 0.088 Positive Predictive Value RNAfold: 0.676 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAfold vs PETfold_2.0(seed) Matthews Correlation Coefficient RNAfold: 0.868 PETfold_2.0(seed): 0.866 Sensitivity RNAfold: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value RNAfold: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAfold: 0.752 Sensitivity PETfold_2.0(20): 0.889 RNAfold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 RNAfold: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAshapes	39 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAshapes: 0.651 Sensitivity CentroidAlifold(20): 0.728 RNAshapes: 0.672 Positive Predictive Value CentroidAlifold(20): 0.901 RNAshapes: 0.638 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNAshapes: 0.596 Sensitivity PETfold_pre2.0(seed): 0.826 RNAshapes: 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNAshapes: 0.583 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	47 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.760 RNAshapes: 0.618 Sensitivity ContextFold: 0.742 RNAshapes: 0.638 Positive Predictive Value ContextFold: 0.784 RNAshapes: 0.605 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.769 RNAshapes: 0.685 Sensitivity MXScarna(seed): 0.727 RNAshapes: 0.704 Positive Predictive Value MXScarna(seed): 0.819 RNAshapes: 0.673 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAshapes: 0.685 Sensitivity RNAalifold(20): 0.704 RNAshapes: 0.694 Positive Predictive Value RNAalifold(20): 0.891 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAshapes: 0.564 Sensitivity PETfold_pre2.0(20): 0.776 RNAshapes: 0.600 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	15 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.812 RNAshapes: 0.669 Sensitivity PPfold(20): 0.753 RNAshapes: 0.678 Positive Predictive Value PPfold(20): 0.880 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	55 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.742 RNAshapes: 0.633 Sensitivity IPknot: 0.729 RNAshapes: 0.653 Positive Predictive Value IPknot: 0.759 RNAshapes: 0.621 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.755 RNAshapes: 0.685 Sensitivity MXScarna(20): 0.720 RNAshapes: 0.694 Positive Predictive Value MXScarna(20): 0.796 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.751 RNAshapes: 0.685 Sensitivity RNASampler(20): 0.663 RNAshapes: 0.694 Positive Predictive Value RNASampler(20): 0.856 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.773 RNAshapes: 0.669 Sensitivity TurboFold(20): 0.737 RNAshapes: 0.678 Positive Predictive Value TurboFold(20): 0.817 RNAshapes: 0.668 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	60 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNAshapes: 0.669 Sensitivity CentroidAlifold(seed): 0.535 RNAshapes: 0.693 Positive Predictive Value CentroidAlifold(seed): 0.884 RNAshapes: 0.653 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 6.58294707158e-07	133 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.737 RNAshapes: 0.697 Sensitivity CentroidFold: 0.736 RNAshapes: 0.717 Positive Predictive Value CentroidFold: 0.743 RNAshapes: 0.683 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.755 RNAshapes: 0.714 Sensitivity Sfold: 0.746 RNAshapes: 0.731 Positive Predictive Value Sfold: 0.769 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAshapes: 0.667 Sensitivity CentroidHomfold‑LAST: 0.629 RNAshapes: 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.734 RNAshapes: 0.714 Sensitivity Contrafold: 0.755 RNAshapes: 0.731 Positive Predictive Value Contrafold: 0.720 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.683 RNAalifold(seed): 0.680 Sensitivity RNAshapes: 0.707 RNAalifold(seed): 0.525 Positive Predictive Value RNAshapes: 0.666 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.090340659959	115 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.717 RNAshapes: 0.709 Sensitivity MaxExpect: 0.733 RNAshapes: 0.728 Positive Predictive Value MaxExpect: 0.707 RNAshapes: 0.697 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.03703286746e-07	135 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.737 RNAshapes: 0.714 Sensitivity HotKnots: 0.761 RNAshapes: 0.731 Positive Predictive Value HotKnots: 0.719 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.738 RNAshapes: 0.714 Sensitivity UNAFold: 0.756 RNAshapes: 0.731 Positive Predictive Value UNAFold: 0.727 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.698 RNAshapes: 0.691 Sensitivity ProbKnot: 0.732 RNAshapes: 0.714 Positive Predictive Value ProbKnot: 0.670 RNAshapes: 0.675 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 4.87628608759e-06	34 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.693 RNAshapes: 0.685 Sensitivity Murlet(20): 0.594 RNAshapes: 0.694 Positive Predictive Value Murlet(20): 0.815 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.17043408065e-05	135 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.718 RNAshapes: 0.714 Sensitivity PknotsRG: 0.744 RNAshapes: 0.731 Positive Predictive Value PknotsRG: 0.698 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 0.00181847574797	135 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.726 RNAshapes: 0.714 Sensitivity RNAfold: 0.747 RNAshapes: 0.731 Positive Predictive Value RNAfold: 0.711 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.85233844192e-08		= Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.710 RNAshapes: 0.708 Sensitivity Fold: 0.740 RNAshapes: 0.729 Positive Predictive Value Fold: 0.687 RNAshapes: 0.694 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.686772471119	- TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAshapes: 0.628 Sensitivity TurboFold(seed): 0.615 RNAshapes: 0.634 Positive Predictive Value TurboFold(seed): 0.691 RNAshapes: 0.631 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.69833448636e-08	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.726 Afold: 0.717 Sensitivity RNAshapes: 0.746 Afold: 0.746 Positive Predictive Value RNAshapes: 0.714 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.75828119249e-07	= Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.686 RNAshapes: 0.685 Sensitivity Carnac(20): 0.518 RNAshapes: 0.694 Positive Predictive Value Carnac(20): 0.915 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.777738600652	= RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.667 RSpredict(20): 0.660 Sensitivity RNAshapes: 0.686 RSpredict(20): 0.597 Positive Predictive Value RNAshapes: 0.654 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.0265675133358	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.714 RNAsubopt: 0.703 Sensitivity RNAshapes: 0.731 RNAsubopt: 0.730 Positive Predictive Value RNAshapes: 0.705 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.741 Cylofold: 0.701 Sensitivity RNAshapes: 0.748 Cylofold: 0.686 Positive Predictive Value RNAshapes: 0.742 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.713 McQFold: 0.671 Sensitivity RNAshapes: 0.729 McQFold: 0.677 Positive Predictive Value RNAshapes: 0.703 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.618 RNASLOpt: 0.580 Sensitivity RNAshapes: 0.638 RNASLOpt: 0.559 Positive Predictive Value RNAshapes: 0.605 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.763 Pknots: 0.705 Sensitivity RNAshapes: 0.768 Pknots: 0.732 Positive Predictive Value RNAshapes: 0.766 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.704 CRWrnafold: 0.683 Sensitivity RNAshapes: 0.710 CRWrnafold: 0.690 Positive Predictive Value RNAshapes: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.42533765126e-05	+ RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.734 Multilign(20): 0.652 Sensitivity RNAshapes: 0.733 Multilign(20): 0.624 Positive Predictive Value RNAshapes: 0.743 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.747 RNASampler(seed): 0.728 Sensitivity RNAshapes: 0.771 RNASampler(seed): 0.634 Positive Predictive Value RNAshapes: 0.730 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.88234616094e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.806 Alterna: 0.767 Sensitivity RNAshapes: 0.803 Alterna: 0.777 Positive Predictive Value RNAshapes: 0.819 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.685 Mastr(20): 0.620 Sensitivity RNAshapes: 0.694 Mastr(20): 0.473 Positive Predictive Value RNAshapes: 0.682 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.731 Vsfold4: 0.635 Sensitivity RNAshapes: 0.744 Vsfold4: 0.625 Positive Predictive Value RNAshapes: 0.725 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.746 Murlet(seed): 0.594 Sensitivity RNAshapes: 0.750 Murlet(seed): 0.418 Positive Predictive Value RNAshapes: 0.749 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.756 MCFold: 0.622 Sensitivity RNAshapes: 0.768 MCFold: 0.663 Positive Predictive Value RNAshapes: 0.753 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.729 Vsfold5: 0.593 Sensitivity RNAshapes: 0.742 Vsfold5: 0.595 Positive Predictive Value RNAshapes: 0.724 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.625 RNAwolf: 0.467 Sensitivity RNAshapes: 0.649 RNAwolf: 0.481 Positive Predictive Value RNAshapes: 0.609 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: 0.659 CMfinder(20): 0.652 Sensitivity RNAshapes: 0.667 CMfinder(20): 0.518 Positive Predictive Value RNAshapes: 0.661 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.663 NanoFolder: 0.394 Sensitivity RNAshapes: 0.683 NanoFolder: 0.485 Positive Predictive Value RNAshapes: 0.651 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.793 RDfolder: 0.677 Sensitivity RNAshapes: 0.787 RDfolder: 0.637 Positive Predictive Value RNAshapes: 0.810 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.680 RSpredict(seed): 0.316 Sensitivity RNAshapes: 0.703 RSpredict(seed): 0.179 Positive Predictive Value RNAshapes: 0.663 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.649 RNAshapes: 0.640 Sensitivity Multilign(seed): 0.591 RNAshapes: 0.639 Positive Predictive Value Multilign(seed): 0.724 RNAshapes: 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.633 PPfold(seed): 0.094 Sensitivity RNAshapes: 0.638 PPfold(seed): 0.019 Positive Predictive Value RNAshapes: 0.637 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.751 Carnac(seed): 0.277 Sensitivity RNAshapes: 0.755 Carnac(seed): 0.078 Positive Predictive Value RNAshapes: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.683 Mastr(seed): 0.279 Sensitivity RNAshapes: 0.702 Mastr(seed): 0.088 Positive Predictive Value RNAshapes: 0.672 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNAshapes: 0.612 Sensitivity PETfold_2.0(seed): 0.845 RNAshapes: 0.638 Positive Predictive Value PETfold_2.0(seed): 0.891 RNAshapes: 0.597 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAshapes: 0.234 Sensitivity PETfold_2.0(20): 0.889 RNAshapes: 0.259 Positive Predictive Value PETfold_2.0(20): 0.923 RNAshapes: 0.226 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Fold	31 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.793 Fold: 0.664 Sensitivity CentroidAlifold(20): 0.704 Fold: 0.696 Positive Predictive Value CentroidAlifold(20): 0.898 Fold: 0.640 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 Fold: 0.590 Sensitivity PETfold_pre2.0(seed): 0.841 Fold: 0.616 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Fold: 0.567 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	49 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.680 Fold: 0.528 Sensitivity ContextFold: 0.671 Fold: 0.561 Positive Predictive Value ContextFold: 0.689 Fold: 0.499 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.774 Fold: 0.663 Sensitivity MXScarna(seed): 0.739 Fold: 0.689 Positive Predictive Value MXScarna(seed): 0.812 Fold: 0.640 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.762 Fold: 0.694 Sensitivity RNAalifold(20): 0.669 Fold: 0.715 Positive Predictive Value RNAalifold(20): 0.872 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Fold: 0.564 Sensitivity PETfold_pre2.0(20): 0.776 Fold: 0.606 Positive Predictive Value PETfold_pre2.0(20): 0.815 Fold: 0.534 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	15 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.812 Fold: 0.634 Sensitivity PPfold(20): 0.753 Fold: 0.656 Positive Predictive Value PPfold(20): 0.880 Fold: 0.622 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	57 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.675 Fold: 0.542 Sensitivity IPknot: 0.645 Fold: 0.574 Positive Predictive Value IPknot: 0.707 Fold: 0.513 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.736 Fold: 0.694 Sensitivity MXScarna(20): 0.697 Fold: 0.715 Positive Predictive Value MXScarna(20): 0.782 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.721 Fold: 0.694 Sensitivity RNASampler(20): 0.625 Fold: 0.715 Positive Predictive Value RNASampler(20): 0.837 Fold: 0.680 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.773 Fold: 0.634 Sensitivity TurboFold(20): 0.737 Fold: 0.656 Positive Predictive Value TurboFold(20): 0.817 Fold: 0.622 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	49 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.736 Fold: 0.659 Sensitivity CentroidAlifold(seed): 0.608 Fold: 0.688 Positive Predictive Value CentroidAlifold(seed): 0.893 Fold: 0.633 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 8.81311508309e-08	113 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.683 Fold: 0.633 Sensitivity CentroidFold: 0.673 Fold: 0.666 Positive Predictive Value CentroidFold: 0.694 Fold: 0.604 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.671 Fold: 0.636 Sensitivity Sfold: 0.674 Fold: 0.668 Positive Predictive Value Sfold: 0.670 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 Fold: 0.642 Sensitivity CentroidHomfold‑LAST: 0.629 Fold: 0.667 Positive Predictive Value CentroidHomfold‑LAST: 0.803 Fold: 0.626 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.668 Fold: 0.636 Sensitivity Contrafold: 0.687 Fold: 0.668 Positive Predictive Value Contrafold: 0.652 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.733 Fold: 0.609 Sensitivity RNAalifold(seed): 0.617 Fold: 0.639 Positive Predictive Value RNAalifold(seed): 0.871 Fold: 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	101 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.655 Fold: 0.636 Sensitivity MaxExpect: 0.673 Fold: 0.668 Positive Predictive Value MaxExpect: 0.638 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.85233844192e-08	99 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.728 Fold: 0.710 Sensitivity HotKnots: 0.758 Fold: 0.740 Positive Predictive Value HotKnots: 0.705 Fold: 0.687 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 8.81311508309e-08	101 UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.653 Fold: 0.636 Sensitivity UNAFold: 0.677 Fold: 0.668 Positive Predictive Value UNAFold: 0.631 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 8.1815824276e-08	93 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.638 Fold: 0.619 Sensitivity ProbKnot: 0.668 Fold: 0.652 Positive Predictive Value ProbKnot: 0.612 Fold: 0.590 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 4.1569883686e-08	24 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.694 Murlet(20): 0.667 Sensitivity Fold: 0.715 Murlet(20): 0.567 Positive Predictive Value Fold: 0.680 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	100 PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.657 Fold: 0.650 Sensitivity PknotsRG: 0.691 Fold: 0.683 Positive Predictive Value PknotsRG: 0.627 Fold: 0.621 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 7.33397498022e-05	101 RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.645 Fold: 0.636 Sensitivity RNAfold: 0.673 Fold: 0.668 Positive Predictive Value RNAfold: 0.620 Fold: 0.608 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 9.291770879e-07	99 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.710 RNAshapes: 0.708 Sensitivity Fold: 0.740 RNAshapes: 0.729 Positive Predictive Value Fold: 0.687 RNAshapes: 0.694 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.686772471119		- TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.647 Fold: 0.532 Sensitivity TurboFold(seed): 0.615 Fold: 0.550 Positive Predictive Value TurboFold(seed): 0.691 Fold: 0.527 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.652 Afold: 0.630 Sensitivity Fold: 0.689 Afold: 0.669 Positive Predictive Value Fold: 0.618 Afold: 0.596 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.694 Carnac(20): 0.646 Sensitivity Fold: 0.715 Carnac(20): 0.470 Positive Predictive Value Fold: 0.680 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.662 RSpredict(20): 0.631 Sensitivity Fold: 0.693 RSpredict(20): 0.569 Positive Predictive Value Fold: 0.638 RSpredict(20): 0.706 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08	= Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.710 RNAsubopt: 0.707 Sensitivity Fold: 0.740 RNAsubopt: 0.738 Positive Predictive Value Fold: 0.687 RNAsubopt: 0.684 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.0336931477392	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.763 Cylofold: 0.701 Sensitivity Fold: 0.777 Cylofold: 0.686 Positive Predictive Value Fold: 0.757 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.635 McQFold: 0.581 Sensitivity Fold: 0.666 McQFold: 0.591 Positive Predictive Value Fold: 0.606 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.596 RNASLOpt: 0.580 Sensitivity Fold: 0.628 RNASLOpt: 0.559 Positive Predictive Value Fold: 0.573 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 1.17668836407e-05	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.785 Pknots: 0.706 Sensitivity Fold: 0.800 Pknots: 0.728 Positive Predictive Value Fold: 0.778 Pknots: 0.693 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.683 Fold: 0.662 Sensitivity CRWrnafold: 0.690 Fold: 0.674 Positive Predictive Value CRWrnafold: 0.689 Fold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.703 Multilign(20): 0.652 Sensitivity Fold: 0.712 Multilign(20): 0.624 Positive Predictive Value Fold: 0.703 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.03356661821e-08	= Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: 0.695 RNASampler(seed): 0.691 Sensitivity Fold: 0.736 RNASampler(seed): 0.589 Positive Predictive Value Fold: 0.664 RNASampler(seed): 0.819 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0100411242504	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.845 Alterna: 0.788 Sensitivity Fold: 0.853 Alterna: 0.801 Positive Predictive Value Fold: 0.846 Alterna: 0.785 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.694 Mastr(20): 0.573 Sensitivity Fold: 0.715 Mastr(20): 0.412 Positive Predictive Value Fold: 0.680 Mastr(20): 0.804 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.758 Vsfold4: 0.629 Sensitivity Fold: 0.780 Vsfold4: 0.622 Positive Predictive Value Fold: 0.743 Vsfold4: 0.645 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.685 Murlet(seed): 0.582 Sensitivity Fold: 0.704 Murlet(seed): 0.405 Positive Predictive Value Fold: 0.674 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.746 MCFold: 0.621 Sensitivity Fold: 0.770 MCFold: 0.656 Positive Predictive Value Fold: 0.731 MCFold: 0.599 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.747 Vsfold5: 0.586 Sensitivity Fold: 0.769 Vsfold5: 0.589 Positive Predictive Value Fold: 0.731 Vsfold5: 0.594 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.549 RNAwolf: 0.436 Sensitivity Fold: 0.582 RNAwolf: 0.446 Positive Predictive Value Fold: 0.520 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.653 CMfinder(20): 0.652 Sensitivity Fold: 0.667 CMfinder(20): 0.518 Positive Predictive Value Fold: 0.650 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.720 NanoFolder: 0.394 Sensitivity Fold: 0.739 NanoFolder: 0.485 Positive Predictive Value Fold: 0.709 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.816 RDfolder: 0.686 Sensitivity Fold: 0.820 RDfolder: 0.647 Positive Predictive Value Fold: 0.821 RDfolder: 0.744 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.658 RSpredict(seed): 0.444 Sensitivity Fold: 0.687 RSpredict(seed): 0.304 Positive Predictive Value Fold: 0.632 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.649 Fold: 0.604 Sensitivity Multilign(seed): 0.591 Fold: 0.615 Positive Predictive Value Multilign(seed): 0.724 Fold: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.625 PPfold(seed): 0.094 Sensitivity Fold: 0.640 PPfold(seed): 0.019 Positive Predictive Value Fold: 0.620 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.652 Carnac(seed): 0.499 Sensitivity Fold: 0.672 Carnac(seed): 0.266 Positive Predictive Value Fold: 0.635 Carnac(seed): 0.941 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.704 Mastr(seed): 0.289 Sensitivity Fold: 0.732 Mastr(seed): 0.095 Positive Predictive Value Fold: 0.683 Mastr(seed): 0.885 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Fold: 0.855 Sensitivity PETfold_2.0(seed): 0.845 Fold: 0.879 Positive Predictive Value PETfold_2.0(seed): 0.891 Fold: 0.836 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Fold: 0.735 Sensitivity PETfold_2.0(20): 0.889 Fold: 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 Fold: 0.700 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
TurboFold(seed)	11 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.690 TurboFold(seed): 0.625 Sensitivity CentroidAlifold(20): 0.576 TurboFold(seed): 0.624 Positive Predictive Value CentroidAlifold(20): 0.832 TurboFold(seed): 0.634 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.24019667966e-08	12 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.789 TurboFold(seed): 0.608 Sensitivity PETfold_pre2.0(seed): 0.721 TurboFold(seed): 0.600 Positive Predictive Value PETfold_pre2.0(seed): 0.867 TurboFold(seed): 0.625 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	8 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.606 TurboFold(seed): 0.576 Sensitivity ContextFold: 0.560 TurboFold(seed): 0.545 Positive Predictive Value ContextFold: 0.665 TurboFold(seed): 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 MXScarna(seed): 0.633 Sensitivity TurboFold(seed): 0.615 MXScarna(seed): 0.580 Positive Predictive Value TurboFold(seed): 0.691 MXScarna(seed): 0.700 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.69659660552e-05	9 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 RNAalifold(20): 0.663 Sensitivity TurboFold(seed): 0.653 RNAalifold(20): 0.602 Positive Predictive Value TurboFold(seed): 0.723 RNAalifold(20): 0.739 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.600 TurboFold(seed): 0.546 Sensitivity PETfold_pre2.0(20): 0.575 TurboFold(seed): 0.553 Positive Predictive Value PETfold_pre2.0(20): 0.632 TurboFold(seed): 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.710 TurboFold(seed): 0.683 Sensitivity PPfold(20): 0.634 TurboFold(seed): 0.653 Positive Predictive Value PPfold(20): 0.801 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.650 TurboFold(seed): 0.624 Sensitivity IPknot: 0.590 TurboFold(seed): 0.590 Positive Predictive Value IPknot: 0.724 TurboFold(seed): 0.670 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.35010831363e-08	9 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 MXScarna(20): 0.621 Sensitivity TurboFold(seed): 0.653 MXScarna(20): 0.579 Positive Predictive Value TurboFold(seed): 0.723 MXScarna(20): 0.676 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.705 TurboFold(seed): 0.683 Sensitivity RNASampler(20): 0.630 TurboFold(seed): 0.653 Positive Predictive Value RNASampler(20): 0.795 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.694 TurboFold(seed): 0.683 Sensitivity TurboFold(20): 0.653 TurboFold(seed): 0.653 Positive Predictive Value TurboFold(20): 0.746 TurboFold(seed): 0.723 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	15 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 TurboFold(seed): 0.653 Sensitivity CentroidAlifold(seed): 0.558 TurboFold(seed): 0.641 Positive Predictive Value CentroidAlifold(seed): 0.916 TurboFold(seed): 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	15 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.665 TurboFold(seed): 0.653 Sensitivity CentroidFold: 0.638 TurboFold(seed): 0.641 Positive Predictive Value CentroidFold: 0.700 TurboFold(seed): 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.48358879813e-06	11 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.666 TurboFold(seed): 0.647 Sensitivity Sfold: 0.611 TurboFold(seed): 0.615 Positive Predictive Value Sfold: 0.734 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.40944795717e-06	10 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.666 CentroidHomfold‑LAST: 0.649 Sensitivity TurboFold(seed): 0.635 CentroidHomfold‑LAST: 0.618 Positive Predictive Value TurboFold(seed): 0.708 CentroidHomfold‑LAST: 0.692 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.8740818951e-06	11 Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.648 TurboFold(seed): 0.647 Sensitivity Contrafold: 0.634 TurboFold(seed): 0.615 Positive Predictive Value Contrafold: 0.672 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.14664306206	10 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.617 TurboFold(seed): 0.611 Sensitivity RNAalifold(seed): 0.462 TurboFold(seed): 0.578 Positive Predictive Value RNAalifold(seed): 0.832 TurboFold(seed): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.106641111385	11 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.647 MaxExpect: 0.600 Sensitivity TurboFold(seed): 0.615 MaxExpect: 0.580 Positive Predictive Value TurboFold(seed): 0.691 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.88760648134e-09	11 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.647 HotKnots: 0.625 Sensitivity TurboFold(seed): 0.615 HotKnots: 0.653 Positive Predictive Value TurboFold(seed): 0.691 HotKnots: 0.609 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.88120811869e-05	11 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.647 UNAFold: 0.579 Sensitivity TurboFold(seed): 0.615 UNAFold: 0.584 Positive Predictive Value TurboFold(seed): 0.691 UNAFold: 0.584 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.02533530638e-08	11 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.647 ProbKnot: 0.590 Sensitivity TurboFold(seed): 0.615 ProbKnot: 0.607 Positive Predictive Value TurboFold(seed): 0.691 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	9 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 Murlet(20): 0.621 Sensitivity TurboFold(seed): 0.653 Murlet(20): 0.546 Positive Predictive Value TurboFold(seed): 0.723 Murlet(20): 0.715 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.662 TurboFold(seed): 0.647 Sensitivity PknotsRG: 0.683 TurboFold(seed): 0.615 Positive Predictive Value PknotsRG: 0.651 TurboFold(seed): 0.691 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39027542218e-05	11 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAfold: 0.629 Sensitivity TurboFold(seed): 0.615 RNAfold: 0.637 Positive Predictive Value TurboFold(seed): 0.691 RNAfold: 0.630 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.56154924607e-07	11 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAshapes: 0.628 Sensitivity TurboFold(seed): 0.615 RNAshapes: 0.634 Positive Predictive Value TurboFold(seed): 0.691 RNAshapes: 0.631 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.69833448636e-08	11 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.647 Fold: 0.532 Sensitivity TurboFold(seed): 0.615 Fold: 0.550 Positive Predictive Value TurboFold(seed): 0.691 Fold: 0.527 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08		? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.665 TurboFold(seed): 0.539 Sensitivity Afold: 0.684 TurboFold(seed): 0.537 Positive Predictive Value Afold: 0.657 TurboFold(seed): 0.554 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): 0.683 Carnac(20): 0.587 Sensitivity TurboFold(seed): 0.653 Carnac(20): 0.407 Positive Predictive Value TurboFold(seed): 0.723 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.625 RSpredict(20): 0.490 Sensitivity TurboFold(seed): 0.624 RSpredict(20): 0.460 Positive Predictive Value TurboFold(seed): 0.634 RSpredict(20): 0.532 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAsubopt: 0.579 Sensitivity TurboFold(seed): 0.615 RNAsubopt: 0.592 Positive Predictive Value TurboFold(seed): 0.691 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.699 TurboFold(seed): 0.697 Sensitivity Cylofold: 0.653 TurboFold(seed): 0.636 Positive Predictive Value Cylofold: 0.762 TurboFold(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.647 McQFold: 0.616 Sensitivity TurboFold(seed): 0.615 McQFold: 0.622 Positive Predictive Value TurboFold(seed): 0.691 McQFold: 0.620 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000969285703303	? TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.576 RNASLOpt: 0.462 Sensitivity TurboFold(seed): 0.545 RNASLOpt: 0.445 Positive Predictive Value TurboFold(seed): 0.619 RNASLOpt: 0.491 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.647 Pknots: 0.536 Sensitivity TurboFold(seed): 0.615 Pknots: 0.569 Positive Predictive Value TurboFold(seed): 0.691 Pknots: 0.517 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	? CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 TurboFold(seed): 0.580 Sensitivity CRWrnafold: 0.595 TurboFold(seed): 0.558 Positive Predictive Value CRWrnafold: 0.591 TurboFold(seed): 0.615 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Multilign(20): 0.680 Sensitivity TurboFold(seed): 0.684 Multilign(20): 0.674 Positive Predictive Value TurboFold(seed): 0.749 Multilign(20): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.547 RNASampler(seed): 0.543 Sensitivity TurboFold(seed): 0.543 RNASampler(seed): 0.457 Positive Predictive Value TurboFold(seed): 0.560 RNASampler(seed): 0.656 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.702 TurboFold(seed): 0.667 Sensitivity Alterna: 0.685 TurboFold(seed): 0.640 Positive Predictive Value Alterna: 0.735 TurboFold(seed): 0.713 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 Mastr(20): 0.626 Sensitivity TurboFold(seed): 0.653 Mastr(20): 0.477 Positive Predictive Value TurboFold(seed): 0.723 Mastr(20): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold4: 0.487 Sensitivity TurboFold(seed): 0.624 Vsfold4: 0.468 Positive Predictive Value TurboFold(seed): 0.688 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.611 Murlet(seed): 0.546 Sensitivity TurboFold(seed): 0.578 Murlet(seed): 0.373 Positive Predictive Value TurboFold(seed): 0.657 Murlet(seed): 0.808 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	+ TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.618 MCFold: 0.470 Sensitivity TurboFold(seed): 0.612 MCFold: 0.519 Positive Predictive Value TurboFold(seed): 0.633 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.666 Vsfold5: 0.438 Sensitivity TurboFold(seed): 0.635 Vsfold5: 0.438 Positive Predictive Value TurboFold(seed): 0.708 Vsfold5: 0.455 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.637 RNAwolf: 0.373 Sensitivity TurboFold(seed): 0.625 RNAwolf: 0.384 Positive Predictive Value TurboFold(seed): 0.658 RNAwolf: 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.532 NanoFolder: 0.410 Sensitivity TurboFold(seed): 0.521 NanoFolder: 0.496 Positive Predictive Value TurboFold(seed): 0.554 NanoFolder: 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.680 RDfolder: 0.528 Sensitivity TurboFold(seed): 0.622 RDfolder: 0.459 Positive Predictive Value TurboFold(seed): 0.760 RDfolder: 0.630 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.653 RSpredict(seed): 0.278 Sensitivity TurboFold(seed): 0.641 RSpredict(seed): 0.154 Positive Predictive Value TurboFold(seed): 0.674 RSpredict(seed): 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.11142658008e-08	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.658 Multilign(seed): 0.595 Sensitivity TurboFold(seed): 0.611 Multilign(seed): 0.537 Positive Predictive Value TurboFold(seed): 0.718 Multilign(seed): 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.624 PPfold(seed): 0.130 Sensitivity TurboFold(seed): 0.590 PPfold(seed): 0.037 Positive Predictive Value TurboFold(seed): 0.670 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 Carnac(seed): 0.288 Sensitivity TurboFold(seed): 0.615 Carnac(seed): 0.084 Positive Predictive Value TurboFold(seed): 0.691 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.615 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.691 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.02510705504e-08	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.967 PETfold_2.0(seed): 0.831 Sensitivity TurboFold(seed): 0.968 PETfold_2.0(seed): 0.806 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Afold	19 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.759 Afold: 0.613 Sensitivity CentroidAlifold(20): 0.654 Afold: 0.640 Positive Predictive Value CentroidAlifold(20): 0.885 Afold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	6 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Afold: 0.538 Sensitivity PETfold_pre2.0(seed): 0.706 Afold: 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.842 Afold: 0.520 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	28 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.513 Afold: 0.508 Sensitivity ContextFold: 0.515 Afold: 0.546 Positive Predictive Value ContextFold: 0.512 Afold: 0.474 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.001244508652	34 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.762 Afold: 0.659 Sensitivity MXScarna(seed): 0.714 Afold: 0.691 Positive Predictive Value MXScarna(seed): 0.818 Afold: 0.634 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.744 Afold: 0.639 Sensitivity RNAalifold(20): 0.648 Afold: 0.658 Positive Predictive Value RNAalifold(20): 0.858 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	4 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.640 Afold: 0.516 Sensitivity PETfold_pre2.0(20): 0.612 Afold: 0.565 Positive Predictive Value PETfold_pre2.0(20): 0.675 Afold: 0.480 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.718 Afold: 0.713 Sensitivity PPfold(20): 0.643 Afold: 0.723 Positive Predictive Value PPfold(20): 0.809 Afold: 0.711 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	34 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.598 Afold: 0.528 Sensitivity IPknot: 0.559 Afold: 0.566 Positive Predictive Value IPknot: 0.642 Afold: 0.495 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.746 Afold: 0.639 Sensitivity MXScarna(20): 0.715 Afold: 0.658 Positive Predictive Value MXScarna(20): 0.783 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.730 Afold: 0.639 Sensitivity RNASampler(20): 0.635 Afold: 0.658 Positive Predictive Value RNASampler(20): 0.844 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.740 Afold: 0.713 Sensitivity TurboFold(20): 0.705 Afold: 0.723 Positive Predictive Value TurboFold(20): 0.782 Afold: 0.711 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	34 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.671 Afold: 0.646 Sensitivity CentroidAlifold(seed): 0.536 Afold: 0.681 Positive Predictive Value CentroidAlifold(seed): 0.845 Afold: 0.620 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 7.5939721025e-08	94 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.649 Afold: 0.563 Sensitivity CentroidFold: 0.643 Afold: 0.610 Positive Predictive Value CentroidFold: 0.656 Afold: 0.520 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.591 Afold: 0.564 Sensitivity Sfold: 0.595 Afold: 0.605 Positive Predictive Value Sfold: 0.587 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.705 Afold: 0.679 Sensitivity CentroidHomfold‑LAST: 0.621 Afold: 0.704 Positive Predictive Value CentroidHomfold‑LAST: 0.810 Afold: 0.663 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.12734318562e-06	105 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.651 Afold: 0.564 Sensitivity Contrafold: 0.676 Afold: 0.605 Positive Predictive Value Contrafold: 0.628 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.675 RNAalifold(seed): 0.644 Sensitivity Afold: 0.714 RNAalifold(seed): 0.491 Positive Predictive Value Afold: 0.642 RNAalifold(seed): 0.850 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	83 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.662 Afold: 0.606 Sensitivity MaxExpect: 0.681 Afold: 0.638 Positive Predictive Value MaxExpect: 0.644 Afold: 0.578 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.745 Afold: 0.717 Sensitivity HotKnots: 0.774 Afold: 0.746 Positive Predictive Value HotKnots: 0.722 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.569 Afold: 0.564 Sensitivity UNAFold: 0.605 Afold: 0.605 Positive Predictive Value UNAFold: 0.536 Afold: 0.526 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.626 Afold: 0.604 Sensitivity ProbKnot: 0.665 Afold: 0.644 Positive Predictive Value ProbKnot: 0.592 Afold: 0.568 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.677 Afold: 0.639 Sensitivity Murlet(20): 0.571 Afold: 0.658 Positive Predictive Value Murlet(20): 0.807 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.0871064633e-07	105 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.564 PknotsRG: 0.551 Sensitivity Afold: 0.605 PknotsRG: 0.593 Positive Predictive Value Afold: 0.526 PknotsRG: 0.513 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.564 RNAfold: 0.562 Sensitivity Afold: 0.605 RNAfold: 0.603 Positive Predictive Value Afold: 0.526 RNAfold: 0.524 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 5.84585956207e-05	101 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.726 Afold: 0.717 Sensitivity RNAshapes: 0.746 Afold: 0.746 Positive Predictive Value RNAshapes: 0.714 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.75828119249e-07	67 Fold vs Afold Matthews Correlation Coefficient Fold: 0.652 Afold: 0.630 Sensitivity Fold: 0.689 Afold: 0.669 Positive Predictive Value Fold: 0.618 Afold: 0.596 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 4.1569883686e-08	5 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.665 TurboFold(seed): 0.539 Sensitivity Afold: 0.684 TurboFold(seed): 0.537 Positive Predictive Value Afold: 0.657 TurboFold(seed): 0.554 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		- Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.703 Afold: 0.639 Sensitivity Carnac(20): 0.512 Afold: 0.658 Positive Predictive Value Carnac(20): 0.968 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	- RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.663 Afold: 0.621 Sensitivity RSpredict(20): 0.622 Afold: 0.647 Positive Predictive Value RSpredict(20): 0.712 Afold: 0.601 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 9.11938533333e-08	- RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.723 Afold: 0.717 Sensitivity RNAsubopt: 0.751 Afold: 0.746 Positive Predictive Value RNAsubopt: 0.703 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.27481660653e-07	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.754 Cylofold: 0.700 Sensitivity Afold: 0.769 Cylofold: 0.685 Positive Predictive Value Afold: 0.746 Cylofold: 0.724 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.562 McQFold: 0.473 Sensitivity Afold: 0.603 McQFold: 0.451 Positive Predictive Value Afold: 0.525 McQFold: 0.497 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.637 RNASLOpt: 0.628 Sensitivity Afold: 0.671 RNASLOpt: 0.634 Positive Predictive Value Afold: 0.613 RNASLOpt: 0.631 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000305895979941	+ Afold vs Pknots Matthews Correlation Coefficient Afold: 0.772 Pknots: 0.746 Sensitivity Afold: 0.788 Pknots: 0.775 Positive Predictive Value Afold: 0.765 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.728 CRWrnafold: 0.652 Sensitivity Afold: 0.756 CRWrnafold: 0.669 Positive Predictive Value Afold: 0.710 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.630 Multilign(20): 0.573 Sensitivity Afold: 0.633 Multilign(20): 0.531 Positive Predictive Value Afold: 0.637 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.797 RNASampler(seed): 0.755 Sensitivity Afold: 0.822 RNASampler(seed): 0.668 Positive Predictive Value Afold: 0.778 RNASampler(seed): 0.860 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.810 Alterna: 0.778 Sensitivity Afold: 0.820 Alterna: 0.785 Positive Predictive Value Afold: 0.810 Alterna: 0.782 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.664 Afold: 0.639 Sensitivity Mastr(20): 0.507 Afold: 0.658 Positive Predictive Value Mastr(20): 0.876 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.71949088499e-07	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.725 Vsfold4: 0.638 Sensitivity Afold: 0.752 Vsfold4: 0.630 Positive Predictive Value Afold: 0.706 Vsfold4: 0.655 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.771 Murlet(seed): 0.613 Sensitivity Afold: 0.777 Murlet(seed): 0.449 Positive Predictive Value Afold: 0.773 Murlet(seed): 0.848 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.768 MCFold: 0.680 Sensitivity Afold: 0.790 MCFold: 0.725 Positive Predictive Value Afold: 0.755 MCFold: 0.650 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.723 Vsfold5: 0.599 Sensitivity Afold: 0.750 Vsfold5: 0.600 Positive Predictive Value Afold: 0.704 Vsfold5: 0.607 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.525 RNAwolf: 0.393 Sensitivity Afold: 0.563 RNAwolf: 0.406 Positive Predictive Value Afold: 0.492 RNAwolf: 0.383 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.818 CMfinder(20): 0.698 Sensitivity Afold: 0.771 CMfinder(20): 0.543 Positive Predictive Value Afold: 0.871 CMfinder(20): 0.905 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.632 NanoFolder: 0.445 Sensitivity Afold: 0.667 NanoFolder: 0.549 Positive Predictive Value Afold: 0.608 NanoFolder: 0.374 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.801 RDfolder: 0.704 Sensitivity Afold: 0.811 RDfolder: 0.663 Positive Predictive Value Afold: 0.803 RDfolder: 0.762 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.650 RSpredict(seed): 0.426 Sensitivity Afold: 0.684 RSpredict(seed): 0.268 Positive Predictive Value Afold: 0.624 RSpredict(seed): 0.685 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.765 Afold: 0.743 Sensitivity Multilign(seed): 0.710 Afold: 0.720 Positive Predictive Value Multilign(seed): 0.835 Afold: 0.779 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.632 PPfold(seed): 0.158 Sensitivity Afold: 0.634 PPfold(seed): 0.048 Positive Predictive Value Afold: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.774 Carnac(seed): 0.341 Sensitivity Afold: 0.780 Carnac(seed): 0.118 Positive Predictive Value Afold: 0.773 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.661 Mastr(seed): 0.344 Sensitivity Afold: 0.691 Mastr(seed): 0.133 Positive Predictive Value Afold: 0.638 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Carnac(20)	39 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Carnac(20): 0.695 Sensitivity CentroidAlifold(20): 0.728 Carnac(20): 0.529 Positive Predictive Value CentroidAlifold(20): 0.901 Carnac(20): 0.918 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Carnac(20): 0.665 Sensitivity PETfold_pre2.0(seed): 0.858 Carnac(20): 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	11 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.781 Carnac(20): 0.612 Sensitivity ContextFold: 0.731 Carnac(20): 0.466 Positive Predictive Value ContextFold: 0.840 Carnac(20): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.19192530585e-08	33 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Carnac(20): 0.685 Sensitivity MXScarna(seed): 0.732 Carnac(20): 0.517 Positive Predictive Value MXScarna(seed): 0.825 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Carnac(20): 0.686 Sensitivity RNAalifold(20): 0.704 Carnac(20): 0.518 Positive Predictive Value RNAalifold(20): 0.891 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Carnac(20): 0.665 Sensitivity PETfold_pre2.0(20): 0.776 Carnac(20): 0.515 Positive Predictive Value PETfold_pre2.0(20): 0.815 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	15 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.812 Carnac(20): 0.638 Sensitivity PPfold(20): 0.753 Carnac(20): 0.491 Positive Predictive Value PPfold(20): 0.880 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	14 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.712 Carnac(20): 0.654 Sensitivity IPknot: 0.678 Carnac(20): 0.516 Positive Predictive Value IPknot: 0.756 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	34 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Carnac(20): 0.686 Sensitivity MXScarna(20): 0.720 Carnac(20): 0.518 Positive Predictive Value MXScarna(20): 0.796 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Carnac(20): 0.686 Sensitivity RNASampler(20): 0.663 Carnac(20): 0.518 Positive Predictive Value RNASampler(20): 0.856 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.773 Carnac(20): 0.638 Sensitivity TurboFold(20): 0.737 Carnac(20): 0.491 Positive Predictive Value TurboFold(20): 0.817 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	39 Carnac(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Carnac(20): 0.695 CentroidAlifold(seed): 0.695 Sensitivity Carnac(20): 0.529 CentroidAlifold(seed): 0.528 Positive Predictive Value Carnac(20): 0.918 CentroidAlifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.88245777838	39 Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.695 CentroidFold: 0.690 Sensitivity Carnac(20): 0.529 CentroidFold: 0.689 Positive Predictive Value Carnac(20): 0.918 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.8192559593	34 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.707 Carnac(20): 0.686 Sensitivity Sfold: 0.683 Carnac(20): 0.518 Positive Predictive Value Sfold: 0.736 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Carnac(20): 0.656 Sensitivity CentroidHomfold‑LAST: 0.744 Carnac(20): 0.515 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Carnac(20): 0.845 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	34 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.686 Contrafold: 0.664 Sensitivity Carnac(20): 0.518 Contrafold: 0.681 Positive Predictive Value Carnac(20): 0.915 Contrafold: 0.654 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Carnac(20): 0.596 Sensitivity RNAalifold(seed): 0.488 Carnac(20): 0.385 Positive Predictive Value RNAalifold(seed): 0.931 Carnac(20): 0.930 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	32 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.690 Carnac(20): 0.684 Sensitivity MaxExpect: 0.693 Carnac(20): 0.516 Positive Predictive Value MaxExpect: 0.694 Carnac(20): 0.912 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.00217949791134	34 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.686 HotKnots: 0.668 Sensitivity Carnac(20): 0.518 HotKnots: 0.692 Positive Predictive Value Carnac(20): 0.915 HotKnots: 0.651 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.3082811195e-06	34 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.692 Carnac(20): 0.686 Sensitivity UNAFold: 0.701 Carnac(20): 0.518 Positive Predictive Value UNAFold: 0.689 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.58638884049e-05	24 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.679 Carnac(20): 0.646 Sensitivity ProbKnot: 0.700 Carnac(20): 0.470 Positive Predictive Value ProbKnot: 0.664 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	34 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.693 Carnac(20): 0.686 Sensitivity Murlet(20): 0.594 Carnac(20): 0.518 Positive Predictive Value Murlet(20): 0.815 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.57295429596e-06	34 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.687 Carnac(20): 0.686 Sensitivity PknotsRG: 0.709 Carnac(20): 0.518 Positive Predictive Value PknotsRG: 0.673 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.903713469855	34 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.686 RNAfold: 0.677 Sensitivity Carnac(20): 0.518 RNAfold: 0.694 Positive Predictive Value Carnac(20): 0.915 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 2.16217446969e-05	34 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.686 RNAshapes: 0.685 Sensitivity Carnac(20): 0.518 RNAshapes: 0.694 Positive Predictive Value Carnac(20): 0.915 RNAshapes: 0.682 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.777738600652	24 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.694 Carnac(20): 0.646 Sensitivity Fold: 0.715 Carnac(20): 0.470 Positive Predictive Value Fold: 0.680 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 Carnac(20): 0.587 Sensitivity TurboFold(seed): 0.653 Carnac(20): 0.407 Positive Predictive Value TurboFold(seed): 0.723 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	20 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.703 Afold: 0.639 Sensitivity Carnac(20): 0.512 Afold: 0.658 Positive Predictive Value Carnac(20): 0.968 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08		+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.693 RSpredict(20): 0.660 Sensitivity Carnac(20): 0.526 RSpredict(20): 0.597 Positive Predictive Value Carnac(20): 0.917 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.686 RNAsubopt: 0.660 Sensitivity Carnac(20): 0.518 RNAsubopt: 0.684 Positive Predictive Value Carnac(20): 0.915 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.715 Carnac(20): 0.687 Sensitivity Cylofold: 0.713 Carnac(20): 0.527 Positive Predictive Value Cylofold: 0.725 Carnac(20): 0.905 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.686 McQFold: 0.641 Sensitivity Carnac(20): 0.518 McQFold: 0.648 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	- RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Carnac(20): 0.612 Sensitivity RNASLOpt: 0.616 Carnac(20): 0.466 Positive Predictive Value RNASLOpt: 0.662 Carnac(20): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.11209877853e-08	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.703 Pknots: 0.619 Sensitivity Carnac(20): 0.543 Pknots: 0.663 Positive Predictive Value Carnac(20): 0.918 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Carnac(20): 0.620 Sensitivity CRWrnafold: 0.683 Carnac(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 Carnac(20): 0.828 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.652 Carnac(20): 0.630 Sensitivity Multilign(20): 0.624 Carnac(20): 0.475 Positive Predictive Value Multilign(20): 0.692 Carnac(20): 0.848 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.95929133067e-07	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Carnac(20): 0.658 Sensitivity RNASampler(seed): 0.604 Carnac(20): 0.465 Positive Predictive Value RNASampler(seed): 0.748 Carnac(20): 0.935 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.788 Alterna: 0.671 Sensitivity Carnac(20): 0.649 Alterna: 0.680 Positive Predictive Value Carnac(20): 0.966 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.686 Mastr(20): 0.620 Sensitivity Carnac(20): 0.518 Mastr(20): 0.473 Positive Predictive Value Carnac(20): 0.915 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.695 Vsfold4: 0.561 Sensitivity Carnac(20): 0.528 Vsfold4: 0.556 Positive Predictive Value Carnac(20): 0.920 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.611 Murlet(seed): 0.557 Sensitivity Carnac(20): 0.401 Murlet(seed): 0.355 Positive Predictive Value Carnac(20): 0.938 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.717 MCFold: 0.499 Sensitivity Carnac(20): 0.561 MCFold: 0.560 Positive Predictive Value Carnac(20): 0.922 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.695 Vsfold5: 0.494 Sensitivity Carnac(20): 0.528 Vsfold5: 0.496 Positive Predictive Value Carnac(20): 0.920 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.686 RNAwolf: 0.438 Sensitivity Carnac(20): 0.542 RNAwolf: 0.454 Positive Predictive Value Carnac(20): 0.873 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.654 CMfinder(20): 0.652 Sensitivity Carnac(20): 0.544 CMfinder(20): 0.518 Positive Predictive Value Carnac(20): 0.795 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.671 NanoFolder: 0.329 Sensitivity Carnac(20): 0.542 NanoFolder: 0.405 Positive Predictive Value Carnac(20): 0.837 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.726 RDfolder: 0.636 Sensitivity Carnac(20): 0.581 RDfolder: 0.602 Positive Predictive Value Carnac(20): 0.916 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.693 RSpredict(seed): 0.230 Sensitivity Carnac(20): 0.526 RSpredict(seed): 0.114 Positive Predictive Value Carnac(20): 0.917 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Carnac(20): 0.608 Sensitivity Multilign(seed): 0.682 Carnac(20): 0.434 Positive Predictive Value Multilign(seed): 0.793 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.654 PPfold(seed): 0.046 Sensitivity Carnac(20): 0.516 PPfold(seed): 0.009 Positive Predictive Value Carnac(20): 0.838 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.672 Carnac(seed): 0.220 Sensitivity Carnac(20): 0.484 Carnac(seed): 0.049 Positive Predictive Value Carnac(20): 0.939 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.686 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.915 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Carnac(20): 0.815 Sensitivity PETfold_2.0(seed): 0.889 Carnac(20): 0.667 Positive Predictive Value PETfold_2.0(seed): 0.923 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Carnac(20): 0.815 Sensitivity PETfold_2.0(20): 0.889 Carnac(20): 0.667 Positive Predictive Value PETfold_2.0(20): 0.923 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RSpredict(20)	38 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 RSpredict(20): 0.657 Sensitivity CentroidAlifold(20): 0.726 RSpredict(20): 0.595 Positive Predictive Value CentroidAlifold(20): 0.901 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.856 RSpredict(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.817 RSpredict(20): 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.897 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	17 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.733 RSpredict(20): 0.593 Sensitivity ContextFold: 0.715 RSpredict(20): 0.539 Positive Predictive Value ContextFold: 0.757 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	38 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.769 RSpredict(20): 0.656 Sensitivity MXScarna(seed): 0.731 RSpredict(20): 0.593 Positive Predictive Value MXScarna(seed): 0.814 RSpredict(20): 0.733 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.779 RSpredict(20): 0.660 Sensitivity RNAalifold(20): 0.704 RSpredict(20): 0.597 Positive Predictive Value RNAalifold(20): 0.866 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 RSpredict(20): 0.625 Sensitivity PETfold_pre2.0(20): 0.763 RSpredict(20): 0.568 Positive Predictive Value PETfold_pre2.0(20): 0.823 RSpredict(20): 0.690 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	21 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.793 RSpredict(20): 0.624 Sensitivity PPfold(20): 0.752 RSpredict(20): 0.572 Positive Predictive Value PPfold(20): 0.841 RSpredict(20): 0.689 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.645 RSpredict(20): 0.627 Sensitivity IPknot: 0.641 RSpredict(20): 0.575 Positive Predictive Value IPknot: 0.656 RSpredict(20): 0.693 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 7.4038562879e-07	39 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.745 RSpredict(20): 0.660 Sensitivity MXScarna(20): 0.719 RSpredict(20): 0.597 Positive Predictive Value MXScarna(20): 0.776 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.737 RSpredict(20): 0.660 Sensitivity RNASampler(20): 0.667 RSpredict(20): 0.597 Positive Predictive Value RNASampler(20): 0.820 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.758 RSpredict(20): 0.624 Sensitivity TurboFold(20): 0.748 RSpredict(20): 0.572 Positive Predictive Value TurboFold(20): 0.773 RSpredict(20): 0.689 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	38 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 RSpredict(20): 0.657 Sensitivity CentroidAlifold(seed): 0.530 RSpredict(20): 0.595 Positive Predictive Value CentroidAlifold(seed): 0.923 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.689 RSpredict(20): 0.657 Sensitivity CentroidFold: 0.687 RSpredict(20): 0.595 Positive Predictive Value CentroidFold: 0.697 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.85233844192e-08	39 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.682 RSpredict(20): 0.660 Sensitivity Sfold: 0.669 RSpredict(20): 0.597 Positive Predictive Value Sfold: 0.700 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 4.83792096436e-08	20 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 RSpredict(20): 0.642 Sensitivity CentroidHomfold‑LAST: 0.726 RSpredict(20): 0.588 Positive Predictive Value CentroidHomfold‑LAST: 0.731 RSpredict(20): 0.708 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	39 RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.660 Contrafold: 0.650 Sensitivity RSpredict(20): 0.597 Contrafold: 0.676 Positive Predictive Value RSpredict(20): 0.735 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000108348164592	22 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.662 RSpredict(20): 0.526 Sensitivity RNAalifold(seed): 0.472 RSpredict(20): 0.465 Positive Predictive Value RNAalifold(seed): 0.932 RSpredict(20): 0.602 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	38 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.666 RSpredict(20): 0.657 Sensitivity MaxExpect: 0.679 RSpredict(20): 0.595 Positive Predictive Value MaxExpect: 0.660 RSpredict(20): 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.000207424631753	39 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.660 HotKnots: 0.646 Sensitivity RSpredict(20): 0.597 HotKnots: 0.678 Positive Predictive Value RSpredict(20): 0.735 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.47427610203e-05	39 RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.660 UNAFold: 0.659 Sensitivity RSpredict(20): 0.597 UNAFold: 0.679 Positive Predictive Value RSpredict(20): 0.735 UNAFold: 0.646 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.788063625903	30 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.650 RSpredict(20): 0.631 Sensitivity ProbKnot: 0.677 RSpredict(20): 0.569 Positive Predictive Value ProbKnot: 0.631 RSpredict(20): 0.706 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.10039559051e-07	39 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.697 RSpredict(20): 0.660 Sensitivity Murlet(20): 0.604 RSpredict(20): 0.597 Positive Predictive Value Murlet(20): 0.810 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.671 RSpredict(20): 0.660 Sensitivity PknotsRG: 0.702 RSpredict(20): 0.597 Positive Predictive Value PknotsRG: 0.648 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 1.34568509467e-07	39 RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.660 RNAfold: 0.655 Sensitivity RSpredict(20): 0.597 RNAfold: 0.681 Positive Predictive Value RSpredict(20): 0.735 RNAfold: 0.636 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000102525955954	39 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.667 RSpredict(20): 0.660 Sensitivity RNAshapes: 0.686 RSpredict(20): 0.597 Positive Predictive Value RNAshapes: 0.654 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.0265675133358	30 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.662 RSpredict(20): 0.631 Sensitivity Fold: 0.693 RSpredict(20): 0.569 Positive Predictive Value Fold: 0.638 RSpredict(20): 0.706 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08	11 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.625 RSpredict(20): 0.490 Sensitivity TurboFold(seed): 0.624 RSpredict(20): 0.460 Positive Predictive Value TurboFold(seed): 0.634 RSpredict(20): 0.532 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.62913390836e-08	20 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.663 Afold: 0.621 Sensitivity RSpredict(20): 0.622 Afold: 0.647 Positive Predictive Value RSpredict(20): 0.712 Afold: 0.601 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 9.11938533333e-08	39 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.693 RSpredict(20): 0.660 Sensitivity Carnac(20): 0.526 RSpredict(20): 0.597 Positive Predictive Value Carnac(20): 0.917 RSpredict(20): 0.735 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08		= RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.660 RNAsubopt: 0.660 Sensitivity RSpredict(20): 0.597 RNAsubopt: 0.693 Positive Predictive Value RSpredict(20): 0.735 RNAsubopt: 0.634 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.686772471119	- Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.711 RSpredict(20): 0.694 Sensitivity Cylofold: 0.714 RSpredict(20): 0.611 Positive Predictive Value Cylofold: 0.717 RSpredict(20): 0.797 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.89611862146e-06	+ RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.660 McQFold: 0.610 Sensitivity RSpredict(20): 0.597 McQFold: 0.626 Positive Predictive Value RSpredict(20): 0.735 McQFold: 0.601 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.593 RNASLOpt: 0.556 Sensitivity RSpredict(20): 0.539 RNASLOpt: 0.559 Positive Predictive Value RSpredict(20): 0.660 RNASLOpt: 0.563 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.42469125465e-07	+ RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.664 Pknots: 0.590 Sensitivity RSpredict(20): 0.600 Pknots: 0.635 Positive Predictive Value RSpredict(20): 0.742 Pknots: 0.557 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.668 RSpredict(20): 0.535 Sensitivity CRWrnafold: 0.683 RSpredict(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	= RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.632 Multilign(20): 0.625 Sensitivity RSpredict(20): 0.565 Multilign(20): 0.611 Positive Predictive Value RSpredict(20): 0.715 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.0508726101154	- RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.612 RSpredict(20): 0.538 Sensitivity RNASampler(seed): 0.566 RSpredict(20): 0.575 Positive Predictive Value RNASampler(seed): 0.668 RSpredict(20): 0.510 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.5296540067e-09	+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.794 Alterna: 0.671 Sensitivity RSpredict(20): 0.718 Alterna: 0.680 Positive Predictive Value RSpredict(20): 0.886 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.660 Mastr(20): 0.626 Sensitivity RSpredict(20): 0.597 Mastr(20): 0.487 Positive Predictive Value RSpredict(20): 0.735 Mastr(20): 0.812 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.669 Vsfold4: 0.540 Sensitivity RSpredict(20): 0.606 Vsfold4: 0.539 Positive Predictive Value RSpredict(20): 0.746 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.554 RSpredict(20): 0.507 Sensitivity Murlet(seed): 0.349 RSpredict(20): 0.445 Positive Predictive Value Murlet(seed): 0.886 RSpredict(20): 0.588 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.691 MCFold: 0.499 Sensitivity RSpredict(20): 0.644 MCFold: 0.560 Positive Predictive Value RSpredict(20): 0.749 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.669 Vsfold5: 0.493 Sensitivity RSpredict(20): 0.606 Vsfold5: 0.499 Positive Predictive Value RSpredict(20): 0.746 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.627 RNAwolf: 0.429 Sensitivity RSpredict(20): 0.575 RNAwolf: 0.446 Positive Predictive Value RSpredict(20): 0.693 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.688 CMfinder(20): 0.660 Sensitivity RSpredict(20): 0.653 CMfinder(20): 0.580 Positive Predictive Value RSpredict(20): 0.731 CMfinder(20): 0.759 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.62909925123e-09	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.618 NanoFolder: 0.326 Sensitivity RSpredict(20): 0.573 NanoFolder: 0.417 Positive Predictive Value RSpredict(20): 0.674 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.752 RDfolder: 0.644 Sensitivity RSpredict(20): 0.668 RDfolder: 0.612 Positive Predictive Value RSpredict(20): 0.857 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.664 RSpredict(seed): 0.341 Sensitivity RSpredict(20): 0.601 RSpredict(seed): 0.194 Positive Predictive Value RSpredict(20): 0.736 RSpredict(seed): 0.604 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.669 RSpredict(20): 0.523 Sensitivity Multilign(seed): 0.632 RSpredict(20): 0.486 Positive Predictive Value Multilign(seed): 0.717 RSpredict(20): 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.627 PPfold(seed): 0.053 Sensitivity RSpredict(20): 0.575 PPfold(seed): 0.010 Positive Predictive Value RSpredict(20): 0.693 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.572 Carnac(seed): 0.214 Sensitivity RSpredict(20): 0.508 Carnac(seed): 0.046 Positive Predictive Value RSpredict(20): 0.652 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.660 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.597 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.735 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAsubopt	39 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.808 RNAsubopt: 0.660 Sensitivity CentroidAlifold(20): 0.728 RNAsubopt: 0.694 Positive Predictive Value CentroidAlifold(20): 0.901 RNAsubopt: 0.634 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNAsubopt: 0.635 Sensitivity PETfold_pre2.0(seed): 0.826 RNAsubopt: 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNAsubopt: 0.611 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	47 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.760 RNAsubopt: 0.611 Sensitivity ContextFold: 0.742 RNAsubopt: 0.645 Positive Predictive Value ContextFold: 0.784 RNAsubopt: 0.584 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.769 RNAsubopt: 0.667 Sensitivity MXScarna(seed): 0.727 RNAsubopt: 0.694 Positive Predictive Value MXScarna(seed): 0.819 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.790 RNAsubopt: 0.660 Sensitivity RNAalifold(20): 0.704 RNAsubopt: 0.684 Positive Predictive Value RNAalifold(20): 0.891 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAsubopt: 0.627 Sensitivity PETfold_pre2.0(20): 0.776 RNAsubopt: 0.675 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAsubopt: 0.590 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.812 RNAsubopt: 0.672 Sensitivity PPfold(20): 0.753 RNAsubopt: 0.688 Positive Predictive Value PPfold(20): 0.880 RNAsubopt: 0.665 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	55 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.742 RNAsubopt: 0.630 Sensitivity IPknot: 0.729 RNAsubopt: 0.663 Positive Predictive Value IPknot: 0.759 RNAsubopt: 0.606 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.755 RNAsubopt: 0.660 Sensitivity MXScarna(20): 0.720 RNAsubopt: 0.684 Positive Predictive Value MXScarna(20): 0.796 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.751 RNAsubopt: 0.660 Sensitivity RNASampler(20): 0.663 RNAsubopt: 0.684 Positive Predictive Value RNASampler(20): 0.856 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.773 RNAsubopt: 0.672 Sensitivity TurboFold(20): 0.737 RNAsubopt: 0.688 Positive Predictive Value TurboFold(20): 0.817 RNAsubopt: 0.665 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	60 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNAsubopt: 0.668 Sensitivity CentroidAlifold(seed): 0.535 RNAsubopt: 0.701 Positive Predictive Value CentroidAlifold(seed): 0.884 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 2.63254822069e-07	133 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.737 RNAsubopt: 0.698 Sensitivity CentroidFold: 0.736 RNAsubopt: 0.730 Positive Predictive Value CentroidFold: 0.743 RNAsubopt: 0.674 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.755 RNAsubopt: 0.703 Sensitivity Sfold: 0.746 RNAsubopt: 0.730 Positive Predictive Value Sfold: 0.769 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 RNAsubopt: 0.667 Sensitivity CentroidHomfold‑LAST: 0.629 RNAsubopt: 0.692 Positive Predictive Value CentroidHomfold‑LAST: 0.803 RNAsubopt: 0.649 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.734 RNAsubopt: 0.703 Sensitivity Contrafold: 0.755 RNAsubopt: 0.730 Positive Predictive Value Contrafold: 0.720 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.680 RNAsubopt: 0.651 Sensitivity RNAalifold(seed): 0.525 RNAsubopt: 0.682 Positive Predictive Value RNAalifold(seed): 0.885 RNAsubopt: 0.627 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.85233844192e-08	115 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.717 RNAsubopt: 0.699 Sensitivity MaxExpect: 0.733 RNAsubopt: 0.729 Positive Predictive Value MaxExpect: 0.707 RNAsubopt: 0.677 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.737 RNAsubopt: 0.703 Sensitivity HotKnots: 0.761 RNAsubopt: 0.730 Positive Predictive Value HotKnots: 0.719 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.738 RNAsubopt: 0.703 Sensitivity UNAFold: 0.756 RNAsubopt: 0.730 Positive Predictive Value UNAFold: 0.727 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.698 RNAsubopt: 0.689 Sensitivity ProbKnot: 0.732 RNAsubopt: 0.722 Positive Predictive Value ProbKnot: 0.670 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 1.27481660653e-07	34 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.693 RNAsubopt: 0.660 Sensitivity Murlet(20): 0.594 RNAsubopt: 0.684 Positive Predictive Value Murlet(20): 0.815 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.718 RNAsubopt: 0.703 Sensitivity PknotsRG: 0.744 RNAsubopt: 0.730 Positive Predictive Value PknotsRG: 0.698 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.726 RNAsubopt: 0.703 Sensitivity RNAfold: 0.747 RNAsubopt: 0.730 Positive Predictive Value RNAfold: 0.711 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.714 RNAsubopt: 0.703 Sensitivity RNAshapes: 0.731 RNAsubopt: 0.730 Positive Predictive Value RNAshapes: 0.705 RNAsubopt: 0.683 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 5.62644058675e-08	99 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.710 RNAsubopt: 0.707 Sensitivity Fold: 0.740 RNAsubopt: 0.738 Positive Predictive Value Fold: 0.687 RNAsubopt: 0.684 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 0.0336931477392	11 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.647 RNAsubopt: 0.579 Sensitivity TurboFold(seed): 0.615 RNAsubopt: 0.592 Positive Predictive Value TurboFold(seed): 0.691 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	101 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.723 Afold: 0.717 Sensitivity RNAsubopt: 0.751 Afold: 0.746 Positive Predictive Value RNAsubopt: 0.703 Afold: 0.695 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 1.27481660653e-07	34 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.686 RNAsubopt: 0.660 Sensitivity Carnac(20): 0.518 RNAsubopt: 0.684 Positive Predictive Value Carnac(20): 0.915 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.660 RNAsubopt: 0.660 Sensitivity RSpredict(20): 0.597 RNAsubopt: 0.693 Positive Predictive Value RSpredict(20): 0.735 RNAsubopt: 0.634 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.686772471119		+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.750 Cylofold: 0.701 Sensitivity RNAsubopt: 0.760 Cylofold: 0.686 Positive Predictive Value RNAsubopt: 0.748 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.701 McQFold: 0.671 Sensitivity RNAsubopt: 0.729 McQFold: 0.677 Positive Predictive Value RNAsubopt: 0.681 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.611 RNASLOpt: 0.580 Sensitivity RNAsubopt: 0.645 RNASLOpt: 0.559 Positive Predictive Value RNAsubopt: 0.584 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.744 Pknots: 0.705 Sensitivity RNAsubopt: 0.760 Pknots: 0.732 Positive Predictive Value RNAsubopt: 0.737 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.683 RNAsubopt: 0.666 Sensitivity CRWrnafold: 0.690 RNAsubopt: 0.682 Positive Predictive Value CRWrnafold: 0.689 RNAsubopt: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.32815307575e-07	+ RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.690 Multilign(20): 0.652 Sensitivity RNAsubopt: 0.696 Multilign(20): 0.624 Positive Predictive Value RNAsubopt: 0.692 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	- RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.728 RNAsubopt: 0.714 Sensitivity RNASampler(seed): 0.634 RNAsubopt: 0.749 Positive Predictive Value RNASampler(seed): 0.843 RNAsubopt: 0.688 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.93493077995e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.795 Alterna: 0.767 Sensitivity RNAsubopt: 0.795 Alterna: 0.777 Positive Predictive Value RNAsubopt: 0.805 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.660 Mastr(20): 0.620 Sensitivity RNAsubopt: 0.684 Mastr(20): 0.473 Positive Predictive Value RNAsubopt: 0.643 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.723 Vsfold4: 0.635 Sensitivity RNAsubopt: 0.744 Vsfold4: 0.625 Positive Predictive Value RNAsubopt: 0.709 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.695 Murlet(seed): 0.594 Sensitivity RNAsubopt: 0.709 Murlet(seed): 0.418 Positive Predictive Value RNAsubopt: 0.690 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.734 MCFold: 0.622 Sensitivity RNAsubopt: 0.757 MCFold: 0.663 Positive Predictive Value RNAsubopt: 0.721 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.722 Vsfold5: 0.593 Sensitivity RNAsubopt: 0.743 Vsfold5: 0.595 Positive Predictive Value RNAsubopt: 0.709 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.640 RNAwolf: 0.467 Sensitivity RNAsubopt: 0.677 RNAwolf: 0.481 Positive Predictive Value RNAsubopt: 0.612 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.685 CMfinder(20): 0.652 Sensitivity RNAsubopt: 0.702 CMfinder(20): 0.518 Positive Predictive Value RNAsubopt: 0.678 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.656 NanoFolder: 0.394 Sensitivity RNAsubopt: 0.683 NanoFolder: 0.485 Positive Predictive Value RNAsubopt: 0.638 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.790 RDfolder: 0.677 Sensitivity RNAsubopt: 0.790 RDfolder: 0.637 Positive Predictive Value RNAsubopt: 0.801 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.667 RSpredict(seed): 0.316 Sensitivity RNAsubopt: 0.701 RSpredict(seed): 0.179 Positive Predictive Value RNAsubopt: 0.642 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.649 RNAsubopt: 0.642 Sensitivity Multilign(seed): 0.591 RNAsubopt: 0.644 Positive Predictive Value Multilign(seed): 0.724 RNAsubopt: 0.650 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.635 PPfold(seed): 0.094 Sensitivity RNAsubopt: 0.647 PPfold(seed): 0.019 Positive Predictive Value RNAsubopt: 0.633 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.718 Carnac(seed): 0.277 Sensitivity RNAsubopt: 0.732 Carnac(seed): 0.078 Positive Predictive Value RNAsubopt: 0.712 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.661 Mastr(seed): 0.279 Sensitivity RNAsubopt: 0.690 Mastr(seed): 0.088 Positive Predictive Value RNAsubopt: 0.641 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAsubopt vs PETfold_2.0(seed) Matthews Correlation Coefficient RNAsubopt: 0.887 PETfold_2.0(seed): 0.866 Sensitivity RNAsubopt: 0.897 PETfold_2.0(seed): 0.845 Positive Predictive Value RNAsubopt: 0.881 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAsubopt: 0.798 Sensitivity PETfold_2.0(20): 0.889 RNAsubopt: 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 RNAsubopt: 0.786 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Cylofold	20 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.847 Cylofold: 0.711 Sensitivity CentroidAlifold(20): 0.762 Cylofold: 0.714 Positive Predictive Value CentroidAlifold(20): 0.945 Cylofold: 0.717 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	14 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.854 Cylofold: 0.655 Sensitivity PETfold_pre2.0(seed): 0.811 Cylofold: 0.637 Positive Predictive Value PETfold_pre2.0(seed): 0.905 Cylofold: 0.685 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.55268413083e-08	35 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.783 Cylofold: 0.612 Sensitivity ContextFold: 0.758 Cylofold: 0.598 Positive Predictive Value ContextFold: 0.816 Cylofold: 0.638 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.775 Cylofold: 0.706 Sensitivity MXScarna(seed): 0.734 Cylofold: 0.693 Positive Predictive Value MXScarna(seed): 0.826 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.820 Cylofold: 0.715 Sensitivity RNAalifold(20): 0.732 Cylofold: 0.713 Positive Predictive Value RNAalifold(20): 0.925 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.82974185391e-08	9 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.882 Cylofold: 0.728 Sensitivity PETfold_pre2.0(20): 0.846 Cylofold: 0.726 Positive Predictive Value PETfold_pre2.0(20): 0.924 Cylofold: 0.737 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.873 Cylofold: 0.768 Sensitivity PPfold(20): 0.813 Cylofold: 0.753 Positive Predictive Value PPfold(20): 0.943 Cylofold: 0.792 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.19192530585e-08	42 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.753 Cylofold: 0.626 Sensitivity IPknot: 0.733 Cylofold: 0.615 Positive Predictive Value IPknot: 0.780 Cylofold: 0.649 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.804 Cylofold: 0.715 Sensitivity MXScarna(20): 0.760 Cylofold: 0.713 Positive Predictive Value MXScarna(20): 0.855 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	19 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.789 Cylofold: 0.715 Sensitivity RNASampler(20): 0.691 Cylofold: 0.713 Positive Predictive Value RNASampler(20): 0.906 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	12 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.836 Cylofold: 0.768 Sensitivity TurboFold(20): 0.788 Cylofold: 0.753 Positive Predictive Value TurboFold(20): 0.892 Cylofold: 0.792 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.18141491686e-08	29 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 Cylofold: 0.704 Sensitivity CentroidAlifold(seed): 0.554 Cylofold: 0.694 Positive Predictive Value CentroidAlifold(seed): 0.941 Cylofold: 0.723 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.33397498022e-05	77 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.783 Cylofold: 0.699 Sensitivity CentroidFold: 0.771 Cylofold: 0.686 Positive Predictive Value CentroidFold: 0.802 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.760 Cylofold: 0.701 Sensitivity Sfold: 0.744 Cylofold: 0.686 Positive Predictive Value Sfold: 0.784 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.695 Cylofold: 0.631 Sensitivity CentroidHomfold‑LAST: 0.623 Cylofold: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.785 Cylofold: 0.653 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.780 Cylofold: 0.701 Sensitivity Contrafold: 0.789 Cylofold: 0.686 Positive Predictive Value Contrafold: 0.779 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.666 RNAalifold(seed): 0.664 Sensitivity Cylofold: 0.647 RNAalifold(seed): 0.510 Positive Predictive Value Cylofold: 0.696 RNAalifold(seed): 0.876 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.456379442218	75 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.753 Cylofold: 0.701 Sensitivity MaxExpect: 0.757 Cylofold: 0.686 Positive Predictive Value MaxExpect: 0.757 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.756 Cylofold: 0.701 Sensitivity HotKnots: 0.772 Cylofold: 0.686 Positive Predictive Value HotKnots: 0.749 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.739 Cylofold: 0.701 Sensitivity UNAFold: 0.746 Cylofold: 0.686 Positive Predictive Value UNAFold: 0.741 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.743 Cylofold: 0.698 Sensitivity ProbKnot: 0.766 Cylofold: 0.683 Positive Predictive Value ProbKnot: 0.730 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.739 Cylofold: 0.715 Sensitivity Murlet(20): 0.645 Cylofold: 0.713 Positive Predictive Value Murlet(20): 0.854 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 7.36344111049e-08	75 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.743 Cylofold: 0.701 Sensitivity PknotsRG: 0.757 Cylofold: 0.686 Positive Predictive Value PknotsRG: 0.738 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.738 Cylofold: 0.701 Sensitivity RNAfold: 0.746 Cylofold: 0.686 Positive Predictive Value RNAfold: 0.738 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.741 Cylofold: 0.701 Sensitivity RNAshapes: 0.748 Cylofold: 0.686 Positive Predictive Value RNAshapes: 0.742 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.763 Cylofold: 0.701 Sensitivity Fold: 0.777 Cylofold: 0.686 Positive Predictive Value Fold: 0.757 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.699 TurboFold(seed): 0.697 Sensitivity Cylofold: 0.653 TurboFold(seed): 0.636 Positive Predictive Value Cylofold: 0.762 TurboFold(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	50 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.754 Cylofold: 0.700 Sensitivity Afold: 0.769 Cylofold: 0.685 Positive Predictive Value Afold: 0.746 Cylofold: 0.724 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.715 Carnac(20): 0.687 Sensitivity Cylofold: 0.713 Carnac(20): 0.527 Positive Predictive Value Cylofold: 0.725 Carnac(20): 0.905 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	20 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.711 RSpredict(20): 0.694 Sensitivity Cylofold: 0.714 RSpredict(20): 0.611 Positive Predictive Value Cylofold: 0.717 RSpredict(20): 0.797 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.89611862146e-06	75 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.750 Cylofold: 0.701 Sensitivity RNAsubopt: 0.760 Cylofold: 0.686 Positive Predictive Value RNAsubopt: 0.748 Cylofold: 0.725 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08		- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.752 Cylofold: 0.698 Sensitivity McQFold: 0.738 Cylofold: 0.683 Positive Predictive Value McQFold: 0.774 Cylofold: 0.723 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.622 Cylofold: 0.612 Sensitivity RNASLOpt: 0.598 Cylofold: 0.598 Positive Predictive Value RNASLOpt: 0.658 Cylofold: 0.638 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.00181847574797	- Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.741 Cylofold: 0.729 Sensitivity Pknots: 0.754 Cylofold: 0.710 Positive Predictive Value Pknots: 0.737 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 6.70530687003e-06	- CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.663 Cylofold: 0.651 Sensitivity CRWrnafold: 0.661 Cylofold: 0.639 Positive Predictive Value CRWrnafold: 0.678 Cylofold: 0.677 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 9.10329362739e-05	+ Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.691 Multilign(20): 0.666 Sensitivity Cylofold: 0.682 Multilign(20): 0.619 Positive Predictive Value Cylofold: 0.711 Multilign(20): 0.727 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.39512130982e-06	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.725 RNASampler(seed): 0.664 Sensitivity Cylofold: 0.712 RNASampler(seed): 0.534 Positive Predictive Value Cylofold: 0.747 RNASampler(seed): 0.836 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.790 Alterna: 0.763 Sensitivity Cylofold: 0.770 Alterna: 0.779 Positive Predictive Value Cylofold: 0.821 Alterna: 0.759 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.715 Mastr(20): 0.646 Sensitivity Cylofold: 0.713 Mastr(20): 0.508 Positive Predictive Value Cylofold: 0.725 Mastr(20): 0.829 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.708 Vsfold4: 0.652 Sensitivity Cylofold: 0.697 Vsfold4: 0.637 Positive Predictive Value Cylofold: 0.729 Vsfold4: 0.678 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.652 Murlet(seed): 0.543 Sensitivity Cylofold: 0.633 Murlet(seed): 0.372 Positive Predictive Value Cylofold: 0.683 Murlet(seed): 0.804 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.739 MCFold: 0.631 Sensitivity Cylofold: 0.720 MCFold: 0.665 Positive Predictive Value Cylofold: 0.767 MCFold: 0.612 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.699 Vsfold5: 0.592 Sensitivity Cylofold: 0.685 Vsfold5: 0.592 Positive Predictive Value Cylofold: 0.723 Vsfold5: 0.604 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.625 RNAwolf: 0.505 Sensitivity Cylofold: 0.616 RNAwolf: 0.505 Positive Predictive Value Cylofold: 0.645 RNAwolf: 0.521 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.754 CMfinder(20): 0.652 Sensitivity Cylofold: 0.737 CMfinder(20): 0.518 Positive Predictive Value Cylofold: 0.778 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.621 NanoFolder: 0.438 Sensitivity Cylofold: 0.620 NanoFolder: 0.529 Positive Predictive Value Cylofold: 0.633 NanoFolder: 0.378 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.783 RDfolder: 0.654 Sensitivity Cylofold: 0.763 RDfolder: 0.618 Positive Predictive Value Cylofold: 0.815 RDfolder: 0.709 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.704 RSpredict(seed): 0.266 Sensitivity Cylofold: 0.694 RSpredict(seed): 0.148 Positive Predictive Value Cylofold: 0.723 RSpredict(seed): 0.498 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.672 Cylofold: 0.605 Sensitivity Multilign(seed): 0.615 Cylofold: 0.559 Positive Predictive Value Multilign(seed): 0.748 Cylofold: 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.684 PPfold(seed): 0.107 Sensitivity Cylofold: 0.659 PPfold(seed): 0.016 Positive Predictive Value Cylofold: 0.721 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.684 Carnac(seed): 0.216 Sensitivity Cylofold: 0.662 Carnac(seed): 0.047 Positive Predictive Value Cylofold: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.66763272401e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.706 Mastr(seed): 0.260 Sensitivity Cylofold: 0.693 Mastr(seed): 0.068 Positive Predictive Value Cylofold: 0.729 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-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 PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
McQFold	39 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.808 McQFold: 0.607 Sensitivity CentroidAlifold(20): 0.728 McQFold: 0.622 Positive Predictive Value CentroidAlifold(20): 0.901 McQFold: 0.599 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 McQFold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.841 McQFold: 0.588 Positive Predictive Value PETfold_pre2.0(seed): 0.892 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	48 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.677 McQFold: 0.469 Sensitivity ContextFold: 0.668 McQFold: 0.482 Positive Predictive Value ContextFold: 0.686 McQFold: 0.457 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.786 McQFold: 0.637 Sensitivity MXScarna(seed): 0.749 McQFold: 0.643 Positive Predictive Value MXScarna(seed): 0.825 McQFold: 0.634 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.790 McQFold: 0.641 Sensitivity RNAalifold(20): 0.704 McQFold: 0.648 Positive Predictive Value RNAalifold(20): 0.891 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 McQFold: 0.539 Sensitivity PETfold_pre2.0(20): 0.776 McQFold: 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.815 McQFold: 0.526 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	15 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.812 McQFold: 0.680 Sensitivity PPfold(20): 0.753 McQFold: 0.678 Positive Predictive Value PPfold(20): 0.880 McQFold: 0.691 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	56 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.672 McQFold: 0.491 Sensitivity IPknot: 0.642 McQFold: 0.503 Positive Predictive Value IPknot: 0.705 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.755 McQFold: 0.641 Sensitivity MXScarna(20): 0.720 McQFold: 0.648 Positive Predictive Value MXScarna(20): 0.796 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.751 McQFold: 0.641 Sensitivity RNASampler(20): 0.663 McQFold: 0.648 Positive Predictive Value RNASampler(20): 0.856 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.773 McQFold: 0.680 Sensitivity TurboFold(20): 0.737 McQFold: 0.678 Positive Predictive Value TurboFold(20): 0.817 McQFold: 0.691 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	61 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 McQFold: 0.623 Sensitivity CentroidAlifold(seed): 0.602 McQFold: 0.633 Positive Predictive Value CentroidAlifold(seed): 0.894 McQFold: 0.615 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	136 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.666 McQFold: 0.521 Sensitivity CentroidFold: 0.660 McQFold: 0.502 Positive Predictive Value CentroidFold: 0.674 McQFold: 0.543 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.612 McQFold: 0.501 Sensitivity Sfold: 0.613 McQFold: 0.483 Positive Predictive Value Sfold: 0.611 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.708 McQFold: 0.639 Sensitivity CentroidHomfold‑LAST: 0.629 McQFold: 0.643 Positive Predictive Value CentroidHomfold‑LAST: 0.803 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.661 McQFold: 0.501 Sensitivity Contrafold: 0.683 McQFold: 0.483 Positive Predictive Value Contrafold: 0.639 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.740 McQFold: 0.623 Sensitivity RNAalifold(seed): 0.624 McQFold: 0.635 Positive Predictive Value RNAalifold(seed): 0.879 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.662 McQFold: 0.542 Sensitivity MaxExpect: 0.678 McQFold: 0.550 Positive Predictive Value MaxExpect: 0.647 McQFold: 0.536 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.735 McQFold: 0.671 Sensitivity HotKnots: 0.760 McQFold: 0.677 Positive Predictive Value HotKnots: 0.717 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.588 McQFold: 0.501 Sensitivity UNAFold: 0.619 McQFold: 0.483 Positive Predictive Value UNAFold: 0.559 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.636 McQFold: 0.567 Sensitivity ProbKnot: 0.666 McQFold: 0.581 Positive Predictive Value ProbKnot: 0.610 McQFold: 0.556 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.693 McQFold: 0.641 Sensitivity Murlet(20): 0.594 McQFold: 0.648 Positive Predictive Value Murlet(20): 0.815 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	138 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.573 McQFold: 0.496 Sensitivity PknotsRG: 0.612 McQFold: 0.477 Positive Predictive Value PknotsRG: 0.538 McQFold: 0.517 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.582 McQFold: 0.501 Sensitivity RNAfold: 0.618 McQFold: 0.483 Positive Predictive Value RNAfold: 0.549 McQFold: 0.520 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.713 McQFold: 0.671 Sensitivity RNAshapes: 0.729 McQFold: 0.677 Positive Predictive Value RNAshapes: 0.703 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	100 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.635 McQFold: 0.581 Sensitivity Fold: 0.666 McQFold: 0.591 Positive Predictive Value Fold: 0.606 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.647 McQFold: 0.616 Sensitivity TurboFold(seed): 0.615 McQFold: 0.622 Positive Predictive Value TurboFold(seed): 0.691 McQFold: 0.620 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000969285703303	104 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.562 McQFold: 0.473 Sensitivity Afold: 0.603 McQFold: 0.451 Positive Predictive Value Afold: 0.525 McQFold: 0.497 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.686 McQFold: 0.641 Sensitivity Carnac(20): 0.518 McQFold: 0.648 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	39 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.660 McQFold: 0.610 Sensitivity RSpredict(20): 0.597 McQFold: 0.626 Positive Predictive Value RSpredict(20): 0.735 McQFold: 0.601 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.701 McQFold: 0.671 Sensitivity RNAsubopt: 0.729 McQFold: 0.677 Positive Predictive Value RNAsubopt: 0.681 McQFold: 0.673 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.752 Cylofold: 0.698 Sensitivity McQFold: 0.738 Cylofold: 0.683 Positive Predictive Value McQFold: 0.774 Cylofold: 0.723 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08		= RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.573 McQFold: 0.567 Sensitivity RNASLOpt: 0.553 McQFold: 0.578 Positive Predictive Value RNASLOpt: 0.602 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00108987668019	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.726 Pknots: 0.703 Sensitivity McQFold: 0.717 Pknots: 0.731 Positive Predictive Value McQFold: 0.744 Pknots: 0.687 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.85233844192e-08	= CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.674 McQFold: 0.669 Sensitivity CRWrnafold: 0.681 McQFold: 0.662 Positive Predictive Value CRWrnafold: 0.679 McQFold: 0.688 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.0124164808574	+ McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.672 Multilign(20): 0.652 Sensitivity McQFold: 0.664 Multilign(20): 0.624 Positive Predictive Value McQFold: 0.690 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.17827782533e-05	= RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.728 McQFold: 0.722 Sensitivity RNASampler(seed): 0.634 McQFold: 0.737 Positive Predictive Value RNASampler(seed): 0.843 McQFold: 0.714 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00587767419934	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.807 Alterna: 0.767 Sensitivity McQFold: 0.778 Alterna: 0.777 Positive Predictive Value McQFold: 0.848 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.641 Mastr(20): 0.620 Sensitivity McQFold: 0.648 Mastr(20): 0.473 Positive Predictive Value McQFold: 0.641 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.70530687003e-06	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.697 Vsfold4: 0.632 Sensitivity McQFold: 0.698 Vsfold4: 0.623 Positive Predictive Value McQFold: 0.703 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.722 Murlet(seed): 0.594 Sensitivity McQFold: 0.717 Murlet(seed): 0.418 Positive Predictive Value McQFold: 0.735 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.713 MCFold: 0.620 Sensitivity McQFold: 0.710 MCFold: 0.660 Positive Predictive Value McQFold: 0.725 MCFold: 0.594 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.703 Vsfold5: 0.590 Sensitivity McQFold: 0.702 Vsfold5: 0.592 Positive Predictive Value McQFold: 0.712 Vsfold5: 0.598 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.503 RNAwolf: 0.433 Sensitivity McQFold: 0.517 RNAwolf: 0.443 Positive Predictive Value McQFold: 0.491 RNAwolf: 0.425 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: 0.774 CMfinder(20): 0.652 Sensitivity McQFold: 0.728 CMfinder(20): 0.518 Positive Predictive Value McQFold: 0.830 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.582 NanoFolder: 0.380 Sensitivity McQFold: 0.593 NanoFolder: 0.470 Positive Predictive Value McQFold: 0.582 NanoFolder: 0.321 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.798 RDfolder: 0.677 Sensitivity McQFold: 0.767 RDfolder: 0.637 Positive Predictive Value McQFold: 0.840 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.624 RSpredict(seed): 0.449 Sensitivity McQFold: 0.636 RSpredict(seed): 0.304 Positive Predictive Value McQFold: 0.616 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.661 Multilign(seed): 0.649 Sensitivity McQFold: 0.635 Multilign(seed): 0.591 Positive Predictive Value McQFold: 0.698 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.666 PPfold(seed): 0.094 Sensitivity McQFold: 0.657 PPfold(seed): 0.019 Positive Predictive Value McQFold: 0.684 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.654 Carnac(seed): 0.474 Sensitivity McQFold: 0.656 Carnac(seed): 0.239 Positive Predictive Value McQFold: 0.655 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.656 Mastr(seed): 0.279 Sensitivity McQFold: 0.665 Mastr(seed): 0.088 Positive Predictive Value McQFold: 0.654 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 McQFold: 0.763 Sensitivity PETfold_2.0(seed): 0.845 McQFold: 0.690 Positive Predictive Value PETfold_2.0(seed): 0.891 McQFold: 0.851 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 McQFold: 0.653 Sensitivity PETfold_2.0(20): 0.889 McQFold: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 McQFold: 0.727 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASLOpt	18 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.798 RNASLOpt: 0.559 Sensitivity CentroidAlifold(20): 0.732 RNASLOpt: 0.561 Positive Predictive Value CentroidAlifold(20): 0.874 RNASLOpt: 0.566 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	25 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 RNASLOpt: 0.591 Sensitivity PETfold_pre2.0(seed): 0.826 RNASLOpt: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.913 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	47 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.760 RNASLOpt: 0.580 Sensitivity ContextFold: 0.742 RNASLOpt: 0.559 Positive Predictive Value ContextFold: 0.784 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.711 RNASLOpt: 0.617 Sensitivity MXScarna(seed): 0.658 RNASLOpt: 0.587 Positive Predictive Value MXScarna(seed): 0.776 RNASLOpt: 0.657 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	11 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.759 RNASLOpt: 0.635 Sensitivity RNAalifold(20): 0.688 RNASLOpt: 0.616 Positive Predictive Value RNAalifold(20): 0.842 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	18 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNASLOpt: 0.559 Sensitivity PETfold_pre2.0(20): 0.776 RNASLOpt: 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNASLOpt: 0.566 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	11 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.802 RNASLOpt: 0.635 Sensitivity PPfold(20): 0.749 RNASLOpt: 0.616 Positive Predictive Value PPfold(20): 0.864 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	47 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.729 RNASLOpt: 0.580 Sensitivity IPknot: 0.718 RNASLOpt: 0.559 Positive Predictive Value IPknot: 0.744 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.670 RNASLOpt: 0.635 Sensitivity MXScarna(20): 0.627 RNASLOpt: 0.616 Positive Predictive Value MXScarna(20): 0.723 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.89166989468e-09	11 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.690 RNASLOpt: 0.635 Sensitivity RNASampler(20): 0.616 RNASLOpt: 0.616 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.16131455263e-08	11 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.755 RNASLOpt: 0.635 Sensitivity TurboFold(20): 0.717 RNASLOpt: 0.616 Positive Predictive Value TurboFold(20): 0.800 RNASLOpt: 0.662 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	25 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.666 RNASLOpt: 0.591 Sensitivity CentroidAlifold(seed): 0.475 RNASLOpt: 0.579 Positive Predictive Value CentroidAlifold(seed): 0.941 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	59 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.673 RNASLOpt: 0.582 Sensitivity CentroidFold: 0.670 RNASLOpt: 0.568 Positive Predictive Value CentroidFold: 0.683 RNASLOpt: 0.605 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.690 RNASLOpt: 0.580 Sensitivity Sfold: 0.676 RNASLOpt: 0.559 Positive Predictive Value Sfold: 0.710 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.677 RNASLOpt: 0.605 Sensitivity CentroidHomfold‑LAST: 0.601 RNASLOpt: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.767 RNASLOpt: 0.643 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.664 RNASLOpt: 0.580 Sensitivity Contrafold: 0.684 RNASLOpt: 0.559 Positive Predictive Value Contrafold: 0.651 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNASLOpt: 0.490 Sensitivity RNAalifold(seed): 0.464 RNASLOpt: 0.474 Positive Predictive Value RNAalifold(seed): 0.875 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	47 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.635 RNASLOpt: 0.580 Sensitivity MaxExpect: 0.645 RNASLOpt: 0.559 Positive Predictive Value MaxExpect: 0.632 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.661 RNASLOpt: 0.580 Sensitivity HotKnots: 0.689 RNASLOpt: 0.559 Positive Predictive Value HotKnots: 0.640 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.638 RNASLOpt: 0.580 Sensitivity UNAFold: 0.660 RNASLOpt: 0.559 Positive Predictive Value UNAFold: 0.623 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.633 RNASLOpt: 0.580 Sensitivity ProbKnot: 0.662 RNASLOpt: 0.559 Positive Predictive Value ProbKnot: 0.612 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Murlet(20): 0.625 Sensitivity RNASLOpt: 0.616 Murlet(20): 0.548 Positive Predictive Value RNASLOpt: 0.662 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00207278670317	47 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.653 RNASLOpt: 0.580 Sensitivity PknotsRG: 0.684 RNASLOpt: 0.559 Positive Predictive Value PknotsRG: 0.630 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.652 RNASLOpt: 0.580 Sensitivity RNAfold: 0.672 RNASLOpt: 0.559 Positive Predictive Value RNAfold: 0.638 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.618 RNASLOpt: 0.580 Sensitivity RNAshapes: 0.638 RNASLOpt: 0.559 Positive Predictive Value RNAshapes: 0.605 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.596 RNASLOpt: 0.580 Sensitivity Fold: 0.628 RNASLOpt: 0.559 Positive Predictive Value Fold: 0.573 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 1.17668836407e-05	8 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.576 RNASLOpt: 0.462 Sensitivity TurboFold(seed): 0.545 RNASLOpt: 0.445 Positive Predictive Value TurboFold(seed): 0.619 RNASLOpt: 0.491 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	27 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.637 RNASLOpt: 0.628 Sensitivity Afold: 0.671 RNASLOpt: 0.634 Positive Predictive Value Afold: 0.613 RNASLOpt: 0.631 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000305895979941	11 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Carnac(20): 0.612 Sensitivity RNASLOpt: 0.616 Carnac(20): 0.466 Positive Predictive Value RNASLOpt: 0.662 Carnac(20): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.11209877853e-08	17 RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.593 RNASLOpt: 0.556 Sensitivity RSpredict(20): 0.539 RNASLOpt: 0.559 Positive Predictive Value RSpredict(20): 0.660 RNASLOpt: 0.563 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.42469125465e-07	47 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.611 RNASLOpt: 0.580 Sensitivity RNAsubopt: 0.645 RNASLOpt: 0.559 Positive Predictive Value RNAsubopt: 0.584 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.85233844192e-08	35 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.622 Cylofold: 0.612 Sensitivity RNASLOpt: 0.598 Cylofold: 0.598 Positive Predictive Value RNASLOpt: 0.658 Cylofold: 0.638 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.00181847574797	46 RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.573 McQFold: 0.567 Sensitivity RNASLOpt: 0.553 McQFold: 0.578 Positive Predictive Value RNASLOpt: 0.602 McQFold: 0.564 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00108987668019		+ RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.623 Pknots: 0.577 Sensitivity RNASLOpt: 0.587 Pknots: 0.606 Positive Predictive Value RNASLOpt: 0.672 Pknots: 0.560 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.688 RNASLOpt: 0.660 Sensitivity CRWrnafold: 0.684 RNASLOpt: 0.632 Positive Predictive Value CRWrnafold: 0.702 RNASLOpt: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.49520278558e-07	+ RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.674 Multilign(20): 0.657 Sensitivity RNASLOpt: 0.648 Multilign(20): 0.644 Positive Predictive Value RNASLOpt: 0.711 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1688086697e-05	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.511 RNASampler(seed): 0.371 Sensitivity RNASLOpt: 0.530 RNASampler(seed): 0.290 Positive Predictive Value RNASLOpt: 0.500 RNASampler(seed): 0.483 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	- Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.691 RNASLOpt: 0.643 Sensitivity Alterna: 0.701 RNASLOpt: 0.597 Positive Predictive Value Alterna: 0.697 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Mastr(20): 0.561 Sensitivity RNASLOpt: 0.616 Mastr(20): 0.430 Positive Predictive Value RNASLOpt: 0.662 Mastr(20): 0.741 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.645 Vsfold4: 0.583 Sensitivity RNASLOpt: 0.608 Vsfold4: 0.572 Positive Predictive Value RNASLOpt: 0.694 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.490 Murlet(seed): 0.470 Sensitivity RNASLOpt: 0.474 Murlet(seed): 0.313 Positive Predictive Value RNASLOpt: 0.518 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.593 MCFold: 0.541 Sensitivity RNASLOpt: 0.571 MCFold: 0.576 Positive Predictive Value RNASLOpt: 0.626 MCFold: 0.519 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.641 Vsfold5: 0.507 Sensitivity RNASLOpt: 0.622 Vsfold5: 0.514 Positive Predictive Value RNASLOpt: 0.671 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.582 RNAwolf: 0.441 Sensitivity RNASLOpt: 0.568 RNAwolf: 0.455 Positive Predictive Value RNASLOpt: 0.605 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.733 CMfinder(20): 0.652 Sensitivity RNASLOpt: 0.693 CMfinder(20): 0.518 Positive Predictive Value RNASLOpt: 0.782 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.627 NanoFolder: 0.394 Sensitivity RNASLOpt: 0.592 NanoFolder: 0.485 Positive Predictive Value RNASLOpt: 0.673 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.683 RDfolder: 0.546 Sensitivity RNASLOpt: 0.639 RDfolder: 0.494 Positive Predictive Value RNASLOpt: 0.747 RDfolder: 0.625 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.591 RSpredict(seed): 0.135 Sensitivity RNASLOpt: 0.578 RSpredict(seed): 0.067 Positive Predictive Value RNASLOpt: 0.613 RSpredict(seed): 0.291 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.554 RNASLOpt: 0.454 Sensitivity Multilign(seed): 0.489 RNASLOpt: 0.423 Positive Predictive Value Multilign(seed): 0.638 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.617 PPfold(seed): 0.102 Sensitivity RNASLOpt: 0.587 PPfold(seed): 0.023 Positive Predictive Value RNASLOpt: 0.657 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.534 Carnac(seed): 0.126 Sensitivity RNASLOpt: 0.512 Carnac(seed): 0.016 Positive Predictive Value RNASLOpt: 0.567 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.617 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.587 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.657 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.16042554876e-08	? CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNASLOpt: 0.776 Sensitivity PETfold_2.0(seed): 0.845 RNASLOpt: 0.759 Positive Predictive Value PETfold_2.0(seed): 0.891 RNASLOpt: 0.800 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNASLOpt: 0.600 Sensitivity PETfold_2.0(20): 0.889 RNASLOpt: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 RNASLOpt: 0.615 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Pknots	38 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.821 Pknots: 0.585 Sensitivity CentroidAlifold(20): 0.750 Pknots: 0.631 Positive Predictive Value CentroidAlifold(20): 0.903 Pknots: 0.553 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 Pknots: 0.550 Sensitivity PETfold_pre2.0(seed): 0.826 Pknots: 0.587 Positive Predictive Value PETfold_pre2.0(seed): 0.913 Pknots: 0.525 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.94031556815e-08	44 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.755 Pknots: 0.577 Sensitivity ContextFold: 0.726 Pknots: 0.606 Positive Predictive Value ContextFold: 0.792 Pknots: 0.560 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.789 Pknots: 0.692 Sensitivity MXScarna(seed): 0.746 Pknots: 0.722 Positive Predictive Value MXScarna(seed): 0.841 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.806 Pknots: 0.619 Sensitivity RNAalifold(20): 0.730 Pknots: 0.663 Positive Predictive Value RNAalifold(20): 0.893 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Pknots: 0.466 Sensitivity PETfold_pre2.0(20): 0.776 Pknots: 0.510 Positive Predictive Value PETfold_pre2.0(20): 0.815 Pknots: 0.437 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	15 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.812 Pknots: 0.591 Sensitivity PPfold(20): 0.753 Pknots: 0.621 Positive Predictive Value PPfold(20): 0.880 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	52 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.768 Pknots: 0.606 Sensitivity IPknot: 0.746 Pknots: 0.634 Positive Predictive Value IPknot: 0.798 Pknots: 0.590 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.775 Pknots: 0.619 Sensitivity MXScarna(20): 0.742 Pknots: 0.663 Positive Predictive Value MXScarna(20): 0.815 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.777 Pknots: 0.619 Sensitivity RNASampler(20): 0.693 Pknots: 0.663 Positive Predictive Value RNASampler(20): 0.875 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.773 Pknots: 0.591 Sensitivity TurboFold(20): 0.737 Pknots: 0.621 Positive Predictive Value TurboFold(20): 0.817 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	58 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.700 Pknots: 0.664 Sensitivity CentroidAlifold(seed): 0.542 Pknots: 0.700 Positive Predictive Value CentroidAlifold(seed): 0.911 Pknots: 0.639 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.85233844192e-08	128 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.772 Pknots: 0.689 Sensitivity CentroidFold: 0.764 Pknots: 0.718 Positive Predictive Value CentroidFold: 0.787 Pknots: 0.670 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.790 Pknots: 0.705 Sensitivity Sfold: 0.773 Pknots: 0.732 Positive Predictive Value Sfold: 0.814 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.771 Pknots: 0.666 Sensitivity CentroidHomfold‑LAST: 0.719 Pknots: 0.679 Positive Predictive Value CentroidHomfold‑LAST: 0.835 Pknots: 0.664 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.775 Pknots: 0.705 Sensitivity Contrafold: 0.785 Pknots: 0.732 Positive Predictive Value Contrafold: 0.772 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.725 Pknots: 0.690 Sensitivity RNAalifold(seed): 0.578 Pknots: 0.722 Positive Predictive Value RNAalifold(seed): 0.916 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 6.53888633552e-08	110 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.768 Pknots: 0.699 Sensitivity MaxExpect: 0.772 Pknots: 0.726 Positive Predictive Value MaxExpect: 0.772 Pknots: 0.682 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.771 Pknots: 0.705 Sensitivity HotKnots: 0.787 Pknots: 0.732 Positive Predictive Value HotKnots: 0.763 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.778 Pknots: 0.705 Sensitivity UNAFold: 0.784 Pknots: 0.732 Positive Predictive Value UNAFold: 0.779 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.761 Pknots: 0.695 Sensitivity ProbKnot: 0.782 Pknots: 0.719 Positive Predictive Value ProbKnot: 0.747 Pknots: 0.681 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.716 Pknots: 0.619 Sensitivity Murlet(20): 0.625 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.827 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.758 Pknots: 0.705 Sensitivity PknotsRG: 0.774 Pknots: 0.732 Positive Predictive Value PknotsRG: 0.750 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.766 Pknots: 0.705 Sensitivity RNAfold: 0.776 Pknots: 0.732 Positive Predictive Value RNAfold: 0.763 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.763 Pknots: 0.705 Sensitivity RNAshapes: 0.768 Pknots: 0.732 Positive Predictive Value RNAshapes: 0.766 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	94 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.785 Pknots: 0.706 Sensitivity Fold: 0.800 Pknots: 0.728 Positive Predictive Value Fold: 0.778 Pknots: 0.693 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.647 Pknots: 0.536 Sensitivity TurboFold(seed): 0.615 Pknots: 0.569 Positive Predictive Value TurboFold(seed): 0.691 Pknots: 0.517 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	97 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.772 Pknots: 0.746 Sensitivity Afold: 0.788 Pknots: 0.775 Positive Predictive Value Afold: 0.765 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.85233844192e-08	33 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.703 Pknots: 0.619 Sensitivity Carnac(20): 0.543 Pknots: 0.663 Positive Predictive Value Carnac(20): 0.918 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.664 Pknots: 0.590 Sensitivity RSpredict(20): 0.600 Pknots: 0.635 Positive Predictive Value RSpredict(20): 0.742 Pknots: 0.557 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.744 Pknots: 0.705 Sensitivity RNAsubopt: 0.760 Pknots: 0.732 Positive Predictive Value RNAsubopt: 0.737 Pknots: 0.689 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.741 Cylofold: 0.729 Sensitivity Pknots: 0.754 Cylofold: 0.710 Positive Predictive Value Pknots: 0.737 Cylofold: 0.758 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 6.70530687003e-06	129 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.726 Pknots: 0.703 Sensitivity McQFold: 0.717 Pknots: 0.731 Positive Predictive Value McQFold: 0.744 Pknots: 0.687 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.85233844192e-08	44 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.623 Pknots: 0.577 Sensitivity RNASLOpt: 0.587 Pknots: 0.606 Positive Predictive Value RNASLOpt: 0.672 Pknots: 0.560 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.683 Pknots: 0.631 Sensitivity CRWrnafold: 0.690 Pknots: 0.659 Positive Predictive Value CRWrnafold: 0.689 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.652 Pknots: 0.619 Sensitivity Multilign(20): 0.624 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.692 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.94708346526e-07	+ Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.740 RNASampler(seed): 0.728 Sensitivity Pknots: 0.801 RNASampler(seed): 0.634 Positive Predictive Value Pknots: 0.691 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.84227110139e-07	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.812 Alterna: 0.767 Sensitivity Pknots: 0.820 Alterna: 0.777 Positive Predictive Value Pknots: 0.815 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.655 Pknots: 0.619 Sensitivity Mastr(20): 0.529 Pknots: 0.663 Positive Predictive Value Mastr(20): 0.819 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.729 Vsfold4: 0.674 Sensitivity Pknots: 0.752 Vsfold4: 0.656 Positive Predictive Value Pknots: 0.717 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.683 Murlet(seed): 0.594 Sensitivity Pknots: 0.716 Murlet(seed): 0.418 Positive Predictive Value Pknots: 0.661 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.691 MCFold: 0.622 Sensitivity Pknots: 0.723 MCFold: 0.663 Positive Predictive Value Pknots: 0.671 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.732 Vsfold5: 0.629 Sensitivity Pknots: 0.753 Vsfold5: 0.626 Positive Predictive Value Pknots: 0.721 Vsfold5: 0.645 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.602 RNAwolf: 0.513 Sensitivity Pknots: 0.636 RNAwolf: 0.516 Positive Predictive Value Pknots: 0.581 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 64 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.652 Pknots: 0.618 Sensitivity CMfinder(20): 0.518 Pknots: 0.623 Positive Predictive Value CMfinder(20): 0.831 Pknots: 0.623 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.601 NanoFolder: 0.429 Sensitivity Pknots: 0.624 NanoFolder: 0.516 Positive Predictive Value Pknots: 0.589 NanoFolder: 0.373 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.802 RDfolder: 0.677 Sensitivity Pknots: 0.809 RDfolder: 0.637 Positive Predictive Value Pknots: 0.804 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.668 RSpredict(seed): 0.326 Sensitivity Pknots: 0.704 RSpredict(seed): 0.187 Positive Predictive Value Pknots: 0.643 RSpredict(seed): 0.584 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.649 Pknots: 0.578 Sensitivity Multilign(seed): 0.591 Pknots: 0.601 Positive Predictive Value Multilign(seed): 0.724 Pknots: 0.568 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.604 PPfold(seed): 0.094 Sensitivity Pknots: 0.625 PPfold(seed): 0.019 Positive Predictive Value Pknots: 0.593 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.674 Carnac(seed): 0.277 Sensitivity Pknots: 0.709 Carnac(seed): 0.078 Positive Predictive Value Pknots: 0.648 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.683 Mastr(seed): 0.295 Sensitivity Pknots: 0.716 Mastr(seed): 0.098 Positive Predictive Value Pknots: 0.660 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Pknots: 0.781 Sensitivity PETfold_2.0(seed): 0.845 Pknots: 0.810 Positive Predictive Value PETfold_2.0(seed): 0.891 Pknots: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Pknots: 0.583 Sensitivity PETfold_2.0(20): 0.889 Pknots: 0.630 Positive Predictive Value PETfold_2.0(20): 0.923 Pknots: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CRWrnafold	7 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.819 CRWrnafold: 0.668 Sensitivity CentroidAlifold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value CentroidAlifold(20): 0.930 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.816 CRWrnafold: 0.636 Sensitivity PETfold_pre2.0(seed): 0.761 CRWrnafold: 0.639 Positive Predictive Value PETfold_pre2.0(seed): 0.881 CRWrnafold: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	26 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.799 CRWrnafold: 0.688 Sensitivity ContextFold: 0.762 CRWrnafold: 0.684 Positive Predictive Value ContextFold: 0.844 CRWrnafold: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.85839946686e-08	9 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.705 CRWrnafold: 0.647 Sensitivity MXScarna(seed): 0.660 CRWrnafold: 0.655 Positive Predictive Value MXScarna(seed): 0.761 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.735 CRWrnafold: 0.668 Sensitivity RNAalifold(20): 0.677 CRWrnafold: 0.683 Positive Predictive Value RNAalifold(20): 0.804 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CRWrnafold: 0.663 Sensitivity PETfold_pre2.0(20): 0.707 CRWrnafold: 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 CRWrnafold: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.780 CRWrnafold: 0.668 Sensitivity PPfold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value PPfold(20): 0.844 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.757 CRWrnafold: 0.683 Sensitivity IPknot: 0.731 CRWrnafold: 0.690 Positive Predictive Value IPknot: 0.793 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.668 MXScarna(20): 0.666 Sensitivity CRWrnafold: 0.683 MXScarna(20): 0.634 Positive Predictive Value CRWrnafold: 0.663 MXScarna(20): 0.707 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): 0.740 CRWrnafold: 0.668 Sensitivity RNASampler(20): 0.659 CRWrnafold: 0.683 Positive Predictive Value RNASampler(20): 0.837 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.683 CRWrnafold: 0.668 Sensitivity TurboFold(20): 0.646 CRWrnafold: 0.683 Positive Predictive Value TurboFold(20): 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.678 CRWrnafold: 0.647 Sensitivity CentroidAlifold(seed): 0.473 CRWrnafold: 0.655 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	32 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.737 CRWrnafold: 0.683 Sensitivity CentroidFold: 0.717 CRWrnafold: 0.690 Positive Predictive Value CentroidFold: 0.767 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.711 CRWrnafold: 0.683 Sensitivity Sfold: 0.692 CRWrnafold: 0.690 Positive Predictive Value Sfold: 0.741 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.6410608252e-08	31 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.758 CRWrnafold: 0.674 Sensitivity CentroidHomfold‑LAST: 0.670 CRWrnafold: 0.681 Positive Predictive Value CentroidHomfold‑LAST: 0.866 CRWrnafold: 0.679 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.733 CRWrnafold: 0.683 Sensitivity Contrafold: 0.731 CRWrnafold: 0.690 Positive Predictive Value Contrafold: 0.745 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	32 CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.683 MaxExpect: 0.662 Sensitivity CRWrnafold: 0.690 MaxExpect: 0.667 Positive Predictive Value CRWrnafold: 0.689 MaxExpect: 0.669 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.10039559051e-07	32 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.725 CRWrnafold: 0.683 Sensitivity HotKnots: 0.747 CRWrnafold: 0.690 Positive Predictive Value HotKnots: 0.712 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	32 CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.683 UNAFold: 0.683 Sensitivity CRWrnafold: 0.690 UNAFold: 0.694 Positive Predictive Value CRWrnafold: 0.689 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.706652010983	32 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.683 ProbKnot: 0.667 Sensitivity CRWrnafold: 0.690 ProbKnot: 0.692 Positive Predictive Value CRWrnafold: 0.689 ProbKnot: 0.654 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.27481660653e-07	7 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.677 CRWrnafold: 0.668 Sensitivity Murlet(20): 0.604 CRWrnafold: 0.683 Positive Predictive Value Murlet(20): 0.767 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.720 CRWrnafold: 0.683 Sensitivity PknotsRG: 0.743 CRWrnafold: 0.690 Positive Predictive Value PknotsRG: 0.708 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	32 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.706 CRWrnafold: 0.683 Sensitivity RNAfold: 0.715 CRWrnafold: 0.690 Positive Predictive Value RNAfold: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.83792096436e-08	32 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.704 CRWrnafold: 0.683 Sensitivity RNAshapes: 0.710 CRWrnafold: 0.690 Positive Predictive Value RNAshapes: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.42533765126e-05	32 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.683 Fold: 0.662 Sensitivity CRWrnafold: 0.690 Fold: 0.674 Positive Predictive Value CRWrnafold: 0.689 Fold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 6.53888633552e-08	7 CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 TurboFold(seed): 0.580 Sensitivity CRWrnafold: 0.595 TurboFold(seed): 0.558 Positive Predictive Value CRWrnafold: 0.591 TurboFold(seed): 0.615 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	19 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.728 CRWrnafold: 0.652 Sensitivity Afold: 0.756 CRWrnafold: 0.669 Positive Predictive Value Afold: 0.710 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	7 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Carnac(20): 0.620 Sensitivity CRWrnafold: 0.683 Carnac(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 Carnac(20): 0.828 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.668 RSpredict(20): 0.535 Sensitivity CRWrnafold: 0.683 RSpredict(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.683 RNAsubopt: 0.666 Sensitivity CRWrnafold: 0.690 RNAsubopt: 0.682 Positive Predictive Value CRWrnafold: 0.689 RNAsubopt: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.32815307575e-07	25 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.663 Cylofold: 0.651 Sensitivity CRWrnafold: 0.661 Cylofold: 0.639 Positive Predictive Value CRWrnafold: 0.678 Cylofold: 0.677 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 9.10329362739e-05	31 CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.674 McQFold: 0.669 Sensitivity CRWrnafold: 0.681 McQFold: 0.662 Positive Predictive Value CRWrnafold: 0.679 McQFold: 0.688 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.0124164808574	26 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.688 RNASLOpt: 0.660 Sensitivity CRWrnafold: 0.684 RNASLOpt: 0.632 Positive Predictive Value CRWrnafold: 0.702 RNASLOpt: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.49520278558e-07	32 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.683 Pknots: 0.631 Sensitivity CRWrnafold: 0.690 Pknots: 0.659 Positive Predictive Value CRWrnafold: 0.689 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08		? CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Multilign(20): 0.617 Sensitivity CRWrnafold: 0.683 Multilign(20): 0.616 Positive Predictive Value CRWrnafold: 0.663 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	= CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.673 Alterna: 0.669 Sensitivity CRWrnafold: 0.690 Alterna: 0.690 Positive Predictive Value CRWrnafold: 0.674 Alterna: 0.665 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00148397846487	? CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Mastr(20): 0.649 Sensitivity CRWrnafold: 0.683 Mastr(20): 0.524 Positive Predictive Value CRWrnafold: 0.663 Mastr(20): 0.811 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.683 Vsfold4: 0.580 Sensitivity CRWrnafold: 0.690 Vsfold4: 0.571 Positive Predictive Value CRWrnafold: 0.689 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.682 MCFold: 0.639 Sensitivity CRWrnafold: 0.690 MCFold: 0.670 Positive Predictive Value CRWrnafold: 0.685 MCFold: 0.621 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.678 Vsfold5: 0.525 Sensitivity CRWrnafold: 0.685 Vsfold5: 0.528 Positive Predictive Value CRWrnafold: 0.683 Vsfold5: 0.538 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.683 RNAwolf: 0.552 Sensitivity CRWrnafold: 0.690 RNAwolf: 0.546 Positive Predictive Value CRWrnafold: 0.689 RNAwolf: 0.575 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.687 NanoFolder: 0.542 Sensitivity CRWrnafold: 0.694 NanoFolder: 0.635 Positive Predictive Value CRWrnafold: 0.689 NanoFolder: 0.478 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.703 RDfolder: 0.530 Sensitivity CRWrnafold: 0.704 RDfolder: 0.479 Positive Predictive Value CRWrnafold: 0.717 RDfolder: 0.610 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 RSpredict(seed): 0.126 Sensitivity CRWrnafold: 0.655 RSpredict(seed): 0.059 Positive Predictive Value CRWrnafold: 0.649 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 PPfold(seed): 0.134 Sensitivity CRWrnafold: 0.655 PPfold(seed): 0.034 Positive Predictive Value CRWrnafold: 0.649 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 Carnac(seed): 0.156 Sensitivity CRWrnafold: 0.595 Carnac(seed): 0.025 Positive Predictive Value CRWrnafold: 0.591 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.655 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.649 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(20)	21 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.799 Multilign(20): 0.625 Sensitivity CentroidAlifold(20): 0.721 Multilign(20): 0.611 Positive Predictive Value CentroidAlifold(20): 0.890 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	16 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.898 Multilign(20): 0.620 Sensitivity PETfold_pre2.0(seed): 0.877 Multilign(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.923 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.29018360962e-08	10 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.820 Multilign(20): 0.657 Sensitivity ContextFold: 0.768 Multilign(20): 0.644 Positive Predictive Value ContextFold: 0.881 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.20383511129e-08	15 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.759 Multilign(20): 0.652 Sensitivity MXScarna(seed): 0.717 Multilign(20): 0.624 Positive Predictive Value MXScarna(seed): 0.810 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	15 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.770 Multilign(20): 0.652 Sensitivity RNAalifold(20): 0.685 Multilign(20): 0.624 Positive Predictive Value RNAalifold(20): 0.871 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	16 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.823 Multilign(20): 0.620 Sensitivity PETfold_pre2.0(20): 0.808 Multilign(20): 0.619 Positive Predictive Value PETfold_pre2.0(20): 0.842 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.43573297697e-08	14 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.844 Multilign(20): 0.699 Sensitivity PPfold(20): 0.791 Multilign(20): 0.688 Positive Predictive Value PPfold(20): 0.906 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.39162260866e-08	13 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.727 Multilign(20): 0.681 Sensitivity IPknot: 0.708 Multilign(20): 0.671 Positive Predictive Value IPknot: 0.755 Multilign(20): 0.701 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.59816551561e-08	15 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.750 Multilign(20): 0.652 Sensitivity MXScarna(20): 0.715 Multilign(20): 0.624 Positive Predictive Value MXScarna(20): 0.795 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	15 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.744 Multilign(20): 0.652 Sensitivity RNASampler(20): 0.645 Multilign(20): 0.624 Positive Predictive Value RNASampler(20): 0.864 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	14 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.796 Multilign(20): 0.699 Sensitivity TurboFold(20): 0.762 Multilign(20): 0.688 Positive Predictive Value TurboFold(20): 0.838 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	21 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.685 Multilign(20): 0.625 Sensitivity CentroidAlifold(seed): 0.506 Multilign(20): 0.611 Positive Predictive Value CentroidAlifold(seed): 0.934 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.648 Multilign(20): 0.625 Sensitivity CentroidFold: 0.654 Multilign(20): 0.611 Positive Predictive Value CentroidFold: 0.652 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.88012384877e-08	15 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.693 Multilign(20): 0.652 Sensitivity Sfold: 0.669 Multilign(20): 0.624 Positive Predictive Value Sfold: 0.728 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	14 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Multilign(20): 0.699 Sensitivity CentroidHomfold‑LAST: 0.744 Multilign(20): 0.688 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.30549897711e-08	15 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.673 Multilign(20): 0.652 Sensitivity Contrafold: 0.675 Multilign(20): 0.624 Positive Predictive Value Contrafold: 0.680 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.58152010255e-08	9 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.679 Multilign(20): 0.500 Sensitivity RNAalifold(seed): 0.498 Multilign(20): 0.464 Positive Predictive Value RNAalifold(seed): 0.937 Multilign(20): 0.554 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	15 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.652 MaxExpect: 0.634 Sensitivity Multilign(20): 0.624 MaxExpect: 0.635 Positive Predictive Value Multilign(20): 0.692 MaxExpect: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	15 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.699 Multilign(20): 0.652 Sensitivity HotKnots: 0.707 Multilign(20): 0.624 Positive Predictive Value HotKnots: 0.701 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	15 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.666 Multilign(20): 0.652 Sensitivity UNAFold: 0.667 Multilign(20): 0.624 Positive Predictive Value UNAFold: 0.676 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.40027452735e-08	15 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.652 ProbKnot: 0.646 Sensitivity Multilign(20): 0.624 ProbKnot: 0.659 Positive Predictive Value Multilign(20): 0.692 ProbKnot: 0.645 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.0194307659e-06	15 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.664 Multilign(20): 0.652 Sensitivity Murlet(20): 0.573 Multilign(20): 0.624 Positive Predictive Value Murlet(20): 0.779 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.61878218056e-06	15 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.701 Multilign(20): 0.652 Sensitivity PknotsRG: 0.712 Multilign(20): 0.624 Positive Predictive Value PknotsRG: 0.699 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.679 Multilign(20): 0.652 Sensitivity RNAfold: 0.680 Multilign(20): 0.624 Positive Predictive Value RNAfold: 0.687 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	15 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.734 Multilign(20): 0.652 Sensitivity RNAshapes: 0.733 Multilign(20): 0.624 Positive Predictive Value RNAshapes: 0.743 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	15 Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.703 Multilign(20): 0.652 Sensitivity Fold: 0.712 Multilign(20): 0.624 Positive Predictive Value Fold: 0.703 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.03356661821e-08	8 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Multilign(20): 0.680 Sensitivity TurboFold(seed): 0.684 Multilign(20): 0.674 Positive Predictive Value TurboFold(seed): 0.749 Multilign(20): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.630 Multilign(20): 0.573 Sensitivity Afold: 0.633 Multilign(20): 0.531 Positive Predictive Value Afold: 0.637 Multilign(20): 0.629 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	15 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.652 Carnac(20): 0.630 Sensitivity Multilign(20): 0.624 Carnac(20): 0.475 Positive Predictive Value Multilign(20): 0.692 Carnac(20): 0.848 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.95929133067e-07	21 RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.632 Multilign(20): 0.625 Sensitivity RSpredict(20): 0.565 Multilign(20): 0.611 Positive Predictive Value RSpredict(20): 0.715 Multilign(20): 0.649 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.0508726101154	15 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.690 Multilign(20): 0.652 Sensitivity RNAsubopt: 0.696 Multilign(20): 0.624 Positive Predictive Value RNAsubopt: 0.692 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	13 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.691 Multilign(20): 0.666 Sensitivity Cylofold: 0.682 Multilign(20): 0.619 Positive Predictive Value Cylofold: 0.711 Multilign(20): 0.727 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.39512130982e-06	15 McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.672 Multilign(20): 0.652 Sensitivity McQFold: 0.664 Multilign(20): 0.624 Positive Predictive Value McQFold: 0.690 Multilign(20): 0.692 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.17827782533e-05	10 RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.674 Multilign(20): 0.657 Sensitivity RNASLOpt: 0.648 Multilign(20): 0.644 Positive Predictive Value RNASLOpt: 0.711 Multilign(20): 0.679 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1688086697e-05	15 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.652 Pknots: 0.619 Sensitivity Multilign(20): 0.624 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.692 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.94708346526e-07	7 CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Multilign(20): 0.617 Sensitivity CRWrnafold: 0.683 Multilign(20): 0.616 Positive Predictive Value CRWrnafold: 0.663 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 Multilign(20): 0.667 Sensitivity RNASampler(seed): 0.593 Multilign(20): 0.703 Positive Predictive Value RNASampler(seed): 0.794 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.811 Alterna: 0.750 Sensitivity Multilign(20): 0.811 Alterna: 0.756 Positive Predictive Value Multilign(20): 0.820 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.652 Mastr(20): 0.639 Sensitivity Multilign(20): 0.624 Mastr(20): 0.520 Positive Predictive Value Multilign(20): 0.692 Mastr(20): 0.796 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000114247382482	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.652 Vsfold4: 0.563 Sensitivity Multilign(20): 0.624 Vsfold4: 0.547 Positive Predictive Value Multilign(20): 0.692 Vsfold4: 0.592 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.530 Multilign(20): 0.500 Sensitivity Murlet(seed): 0.344 Multilign(20): 0.464 Positive Predictive Value Murlet(seed): 0.828 Multilign(20): 0.554 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.611 MCFold: 0.512 Sensitivity Multilign(20): 0.597 MCFold: 0.565 Positive Predictive Value Multilign(20): 0.633 MCFold: 0.475 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.652 Vsfold5: 0.495 Sensitivity Multilign(20): 0.624 Vsfold5: 0.493 Positive Predictive Value Multilign(20): 0.692 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.643 RNAwolf: 0.458 Sensitivity Multilign(20): 0.642 RNAwolf: 0.468 Positive Predictive Value Multilign(20): 0.652 RNAwolf: 0.462 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.76416234106e-08	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.672 CMfinder(20): 0.652 Sensitivity Multilign(20): 0.649 CMfinder(20): 0.518 Positive Predictive Value Multilign(20): 0.705 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.731 NanoFolder: 0.329 Sensitivity Multilign(20): 0.726 NanoFolder: 0.405 Positive Predictive Value Multilign(20): 0.742 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.716 RDfolder: 0.584 Sensitivity Multilign(20): 0.694 RDfolder: 0.518 Positive Predictive Value Multilign(20): 0.752 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.625 RSpredict(seed): 0.198 Sensitivity Multilign(20): 0.611 RSpredict(seed): 0.095 Positive Predictive Value Multilign(20): 0.649 RSpredict(seed): 0.432 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Multilign(20): 0.768 Sensitivity Multilign(seed): 0.750 Multilign(20): 0.750 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.798 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.681 PPfold(seed): 0.023 Sensitivity Multilign(20): 0.671 PPfold(seed): 0.003 Positive Predictive Value Multilign(20): 0.701 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.64686604905e-09	+ Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.560 Carnac(seed): 0.269 Sensitivity Multilign(20): 0.524 Carnac(seed): 0.073 Positive Predictive Value Multilign(20): 0.611 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.76570236188e-09	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.652 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.624 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.692 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08	? CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNASampler(seed)	10 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.621 RNASampler(seed): 0.593 Sensitivity CentroidAlifold(20): 0.517 RNASampler(seed): 0.545 Positive Predictive Value CentroidAlifold(20): 0.752 RNASampler(seed): 0.650 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.62913390836e-08	7 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNASampler(seed): 0.390 Sensitivity PETfold_pre2.0(seed): 0.652 RNASampler(seed): 0.323 Positive Predictive Value PETfold_pre2.0(seed): 0.837 RNASampler(seed): 0.481 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.577 RNASampler(seed): 0.371 Sensitivity ContextFold: 0.550 RNASampler(seed): 0.290 Positive Predictive Value ContextFold: 0.611 RNASampler(seed): 0.483 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	19 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.734 RNASampler(seed): 0.728 Sensitivity MXScarna(seed): 0.688 RNASampler(seed): 0.634 Positive Predictive Value MXScarna(seed): 0.791 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.79687093416e-07	9 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 RNAalifold(20): 0.610 Sensitivity RNASampler(seed): 0.604 RNAalifold(20): 0.578 Positive Predictive Value RNASampler(seed): 0.748 RNAalifold(20): 0.651 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.367 PETfold_pre2.0(20): 0.316 Sensitivity RNASampler(seed): 0.349 PETfold_pre2.0(20): 0.313 Positive Predictive Value RNASampler(seed): 0.392 PETfold_pre2.0(20): 0.325 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.617 PPfold(20): 0.609 Sensitivity RNASampler(seed): 0.525 PPfold(20): 0.533 Positive Predictive Value RNASampler(seed): 0.733 PPfold(20): 0.703 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.660 RNASampler(seed): 0.530 Sensitivity IPknot: 0.595 RNASampler(seed): 0.425 Positive Predictive Value IPknot: 0.740 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 MXScarna(20): 0.640 Sensitivity RNASampler(seed): 0.604 MXScarna(20): 0.626 Positive Predictive Value RNASampler(seed): 0.748 MXScarna(20): 0.661 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 RNASampler(20): 0.666 Sensitivity RNASampler(seed): 0.604 RNASampler(20): 0.647 Positive Predictive Value RNASampler(seed): 0.748 RNASampler(20): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.641 RNASampler(seed): 0.617 Sensitivity TurboFold(20): 0.625 RNASampler(seed): 0.525 Positive Predictive Value TurboFold(20): 0.664 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	21 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNASampler(seed): 0.681 Sensitivity CentroidAlifold(seed): 0.631 RNASampler(seed): 0.593 Positive Predictive Value CentroidAlifold(seed): 0.852 RNASampler(seed): 0.789 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.757 RNASampler(seed): 0.681 Sensitivity CentroidFold: 0.749 RNASampler(seed): 0.593 Positive Predictive Value CentroidFold: 0.770 RNASampler(seed): 0.789 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	19 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.785 RNASampler(seed): 0.728 Sensitivity Sfold: 0.771 RNASampler(seed): 0.634 Positive Predictive Value Sfold: 0.805 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	6 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 RNASampler(seed): 0.579 Sensitivity CentroidHomfold‑LAST: 0.620 RNASampler(seed): 0.465 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	19 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.779 RNASampler(seed): 0.728 Sensitivity Contrafold: 0.791 RNASampler(seed): 0.634 Positive Predictive Value Contrafold: 0.772 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.76499031155e-08	19 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 RNAalifold(seed): 0.714 Sensitivity RNASampler(seed): 0.634 RNAalifold(seed): 0.585 Positive Predictive Value RNASampler(seed): 0.843 RNAalifold(seed): 0.878 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	17 MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.747 RNASampler(seed): 0.717 Sensitivity MaxExpect: 0.766 RNASampler(seed): 0.627 Positive Predictive Value MaxExpect: 0.736 RNASampler(seed): 0.827 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.53384937367e-08	19 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.728 HotKnots: 0.717 Sensitivity RNASampler(seed): 0.634 HotKnots: 0.762 Positive Predictive Value RNASampler(seed): 0.843 HotKnots: 0.683 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000512854650149	19 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.740 RNASampler(seed): 0.728 Sensitivity UNAFold: 0.767 RNASampler(seed): 0.634 Positive Predictive Value UNAFold: 0.721 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.23248012054e-07	10 ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.650 RNASampler(seed): 0.604 Sensitivity ProbKnot: 0.700 RNASampler(seed): 0.496 Positive Predictive Value ProbKnot: 0.611 RNASampler(seed): 0.744 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.05332335737e-08	9 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Murlet(20): 0.585 Sensitivity RNASampler(seed): 0.604 Murlet(20): 0.540 Positive Predictive Value RNASampler(seed): 0.748 Murlet(20): 0.639 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.741 RNASampler(seed): 0.728 Sensitivity PknotsRG: 0.771 RNASampler(seed): 0.634 Positive Predictive Value PknotsRG: 0.719 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.30881340954e-06	19 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.763 RNASampler(seed): 0.728 Sensitivity RNAfold: 0.794 RNASampler(seed): 0.634 Positive Predictive Value RNAfold: 0.739 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	19 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.747 RNASampler(seed): 0.728 Sensitivity RNAshapes: 0.771 RNASampler(seed): 0.634 Positive Predictive Value RNAshapes: 0.730 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.88234616094e-08	14 Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: 0.695 RNASampler(seed): 0.691 Sensitivity Fold: 0.736 RNASampler(seed): 0.589 Positive Predictive Value Fold: 0.664 RNASampler(seed): 0.819 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0100411242504	6 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.547 RNASampler(seed): 0.543 Sensitivity TurboFold(seed): 0.543 RNASampler(seed): 0.457 Positive Predictive Value TurboFold(seed): 0.560 RNASampler(seed): 0.656 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	17 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.797 RNASampler(seed): 0.755 Sensitivity Afold: 0.822 RNASampler(seed): 0.668 Positive Predictive Value Afold: 0.778 RNASampler(seed): 0.860 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	9 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Carnac(20): 0.658 Sensitivity RNASampler(seed): 0.604 Carnac(20): 0.465 Positive Predictive Value RNASampler(seed): 0.748 Carnac(20): 0.935 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.612 RSpredict(20): 0.538 Sensitivity RNASampler(seed): 0.566 RSpredict(20): 0.575 Positive Predictive Value RNASampler(seed): 0.668 RSpredict(20): 0.510 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 4.5296540067e-09	19 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.728 RNAsubopt: 0.714 Sensitivity RNASampler(seed): 0.634 RNAsubopt: 0.749 Positive Predictive Value RNASampler(seed): 0.843 RNAsubopt: 0.688 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.93493077995e-08	8 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.725 RNASampler(seed): 0.664 Sensitivity Cylofold: 0.712 RNASampler(seed): 0.534 Positive Predictive Value Cylofold: 0.747 RNASampler(seed): 0.836 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.728 McQFold: 0.722 Sensitivity RNASampler(seed): 0.634 McQFold: 0.737 Positive Predictive Value RNASampler(seed): 0.843 McQFold: 0.714 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00587767419934	4 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.511 RNASampler(seed): 0.371 Sensitivity RNASLOpt: 0.530 RNASampler(seed): 0.290 Positive Predictive Value RNASLOpt: 0.500 RNASampler(seed): 0.483 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	19 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.740 RNASampler(seed): 0.728 Sensitivity Pknots: 0.801 RNASampler(seed): 0.634 Positive Predictive Value Pknots: 0.691 RNASampler(seed): 0.843 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.84227110139e-07	3 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 Multilign(20): 0.667 Sensitivity RNASampler(seed): 0.593 Multilign(20): 0.703 Positive Predictive Value RNASampler(seed): 0.794 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		- Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.874 RNASampler(seed): 0.818 Sensitivity Alterna: 0.859 RNASampler(seed): 0.715 Positive Predictive Value Alterna: 0.896 RNASampler(seed): 0.945 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	? RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Mastr(20): 0.623 Sensitivity RNASampler(seed): 0.604 Mastr(20): 0.439 Positive Predictive Value RNASampler(seed): 0.748 Mastr(20): 0.891 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.752 Vsfold4: 0.688 Sensitivity RNASampler(seed): 0.659 Vsfold4: 0.675 Positive Predictive Value RNASampler(seed): 0.865 Vsfold4: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Murlet(seed): 0.615 Sensitivity RNASampler(seed): 0.634 Murlet(seed): 0.457 Positive Predictive Value RNASampler(seed): 0.843 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.696 MCFold: 0.616 Sensitivity RNASampler(seed): 0.620 MCFold: 0.681 Positive Predictive Value RNASampler(seed): 0.788 MCFold: 0.565 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.752 Vsfold5: 0.732 Sensitivity RNASampler(seed): 0.659 Vsfold5: 0.733 Positive Predictive Value RNASampler(seed): 0.865 Vsfold5: 0.739 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48421610739e-06	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.497 RNAwolf: 0.424 Sensitivity RNASampler(seed): 0.412 RNAwolf: 0.464 Positive Predictive Value RNASampler(seed): 0.608 RNAwolf: 0.397 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.361 NanoFolder: 0.195 Sensitivity RNASampler(seed): 0.282 NanoFolder: 0.254 Positive Predictive Value RNASampler(seed): 0.476 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.798 RDfolder: 0.686 Sensitivity RNASampler(seed): 0.679 RDfolder: 0.617 Positive Predictive Value RNASampler(seed): 0.948 RDfolder: 0.778 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.29277699493e-09	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.689 RSpredict(seed): 0.546 Sensitivity RNASampler(seed): 0.602 RSpredict(seed): 0.406 Positive Predictive Value RNASampler(seed): 0.795 RSpredict(seed): 0.744 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.696 RNASampler(seed): 0.577 Sensitivity Multilign(seed): 0.649 RNASampler(seed): 0.444 Positive Predictive Value Multilign(seed): 0.754 RNASampler(seed): 0.761 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.530 PPfold(seed): 0.164 Sensitivity RNASampler(seed): 0.425 PPfold(seed): 0.059 Positive Predictive Value RNASampler(seed): 0.670 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Carnac(seed): 0.394 Sensitivity RNASampler(seed): 0.634 Carnac(seed): 0.157 Positive Predictive Value RNASampler(seed): 0.843 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Mastr(seed): 0.503 Sensitivity RNASampler(seed): 0.634 Mastr(seed): 0.285 Positive Predictive Value RNASampler(seed): 0.843 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	? RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Alterna	12 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.886 Alterna: 0.658 Sensitivity CentroidAlifold(20): 0.823 Alterna: 0.667 Positive Predictive Value CentroidAlifold(20): 0.958 Alterna: 0.661 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.06323189071e-08	3 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.812 Alterna: 0.648 Sensitivity PETfold_pre2.0(seed): 0.745 Alterna: 0.655 Positive Predictive Value PETfold_pre2.0(seed): 0.891 Alterna: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.782 Alterna: 0.691 Sensitivity ContextFold: 0.757 Alterna: 0.701 Positive Predictive Value ContextFold: 0.820 Alterna: 0.697 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.07842257011e-08	29 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.828 Alterna: 0.757 Sensitivity MXScarna(seed): 0.776 Alterna: 0.765 Positive Predictive Value MXScarna(seed): 0.892 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	13 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.865 Alterna: 0.671 Sensitivity RNAalifold(20): 0.803 Alterna: 0.680 Positive Predictive Value RNAalifold(20): 0.937 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.39551335374e-08	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.842 Alterna: 0.750 Sensitivity PPfold(20): 0.767 Alterna: 0.756 Positive Predictive Value PPfold(20): 0.932 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	22 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.791 Alterna: 0.684 Sensitivity IPknot: 0.754 Alterna: 0.705 Positive Predictive Value IPknot: 0.840 Alterna: 0.679 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	13 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.846 Alterna: 0.671 Sensitivity MXScarna(20): 0.803 Alterna: 0.680 Positive Predictive Value MXScarna(20): 0.897 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	13 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.912 Alterna: 0.671 Sensitivity RNASampler(20): 0.846 Alterna: 0.680 Positive Predictive Value RNASampler(20): 0.986 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.55268413083e-08	4 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.829 Alterna: 0.750 Sensitivity TurboFold(20): 0.800 Alterna: 0.756 Positive Predictive Value TurboFold(20): 0.867 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	28 Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.753 CentroidAlifold(seed): 0.673 Sensitivity Alterna: 0.761 CentroidAlifold(seed): 0.531 Positive Predictive Value Alterna: 0.756 CentroidAlifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	76 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.848 Alterna: 0.750 Sensitivity CentroidFold: 0.827 Alterna: 0.762 Positive Predictive Value CentroidFold: 0.877 Alterna: 0.750 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.827 Alterna: 0.767 Sensitivity Sfold: 0.809 Alterna: 0.777 Positive Predictive Value Sfold: 0.854 Alterna: 0.769 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: 0.810 Alterna: 0.711 Sensitivity CentroidHomfold‑LAST: 0.719 Alterna: 0.734 Positive Predictive Value CentroidHomfold‑LAST: 0.922 Alterna: 0.704 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	89 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.845 Alterna: 0.767 Sensitivity Contrafold: 0.840 Alterna: 0.777 Positive Predictive Value Contrafold: 0.857 Alterna: 0.769 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: 0.844 RNAalifold(seed): 0.743 Sensitivity Alterna: 0.833 RNAalifold(seed): 0.644 Positive Predictive Value Alterna: 0.863 RNAalifold(seed): 0.869 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.95070920198e-08	70 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.815 Alterna: 0.750 Sensitivity MaxExpect: 0.815 Alterna: 0.764 Positive Predictive Value MaxExpect: 0.823 Alterna: 0.749 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.830 Alterna: 0.767 Sensitivity HotKnots: 0.835 Alterna: 0.777 Positive Predictive Value HotKnots: 0.833 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.831 Alterna: 0.767 Sensitivity UNAFold: 0.829 Alterna: 0.777 Positive Predictive Value UNAFold: 0.842 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.819 Alterna: 0.781 Sensitivity ProbKnot: 0.847 Alterna: 0.798 Positive Predictive Value ProbKnot: 0.801 Alterna: 0.776 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): 0.780 Alterna: 0.671 Sensitivity Murlet(20): 0.695 Alterna: 0.680 Positive Predictive Value Murlet(20): 0.882 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	89 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.803 Alterna: 0.767 Sensitivity PknotsRG: 0.808 Alterna: 0.777 Positive Predictive Value PknotsRG: 0.808 Alterna: 0.769 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: 0.817 Alterna: 0.767 Sensitivity RNAfold: 0.820 Alterna: 0.777 Positive Predictive Value RNAfold: 0.824 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.806 Alterna: 0.767 Sensitivity RNAshapes: 0.803 Alterna: 0.777 Positive Predictive Value RNAshapes: 0.819 Alterna: 0.769 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: 0.845 Alterna: 0.788 Sensitivity Fold: 0.853 Alterna: 0.801 Positive Predictive Value Fold: 0.846 Alterna: 0.785 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.702 TurboFold(seed): 0.667 Sensitivity Alterna: 0.685 TurboFold(seed): 0.640 Positive Predictive Value Alterna: 0.735 TurboFold(seed): 0.713 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	69 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.810 Alterna: 0.778 Sensitivity Afold: 0.820 Alterna: 0.785 Positive Predictive Value Afold: 0.810 Alterna: 0.782 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.788 Alterna: 0.671 Sensitivity Carnac(20): 0.649 Alterna: 0.680 Positive Predictive Value Carnac(20): 0.966 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	13 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.794 Alterna: 0.671 Sensitivity RSpredict(20): 0.718 Alterna: 0.680 Positive Predictive Value RSpredict(20): 0.886 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	89 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.795 Alterna: 0.767 Sensitivity RNAsubopt: 0.795 Alterna: 0.777 Positive Predictive Value RNAsubopt: 0.805 Alterna: 0.769 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: 0.790 Alterna: 0.763 Sensitivity Cylofold: 0.770 Alterna: 0.779 Positive Predictive Value Cylofold: 0.821 Alterna: 0.759 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: 0.807 Alterna: 0.767 Sensitivity McQFold: 0.778 Alterna: 0.777 Positive Predictive Value McQFold: 0.848 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.691 RNASLOpt: 0.643 Sensitivity Alterna: 0.701 RNASLOpt: 0.597 Positive Predictive Value Alterna: 0.697 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	89 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.812 Alterna: 0.767 Sensitivity Pknots: 0.820 Alterna: 0.777 Positive Predictive Value Pknots: 0.815 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.673 Alterna: 0.669 Sensitivity CRWrnafold: 0.690 Alterna: 0.690 Positive Predictive Value CRWrnafold: 0.674 Alterna: 0.665 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00148397846487	4 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.811 Alterna: 0.750 Sensitivity Multilign(20): 0.811 Alterna: 0.756 Positive Predictive Value Multilign(20): 0.820 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	14 Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.874 RNASampler(seed): 0.818 Sensitivity Alterna: 0.859 RNASampler(seed): 0.715 Positive Predictive Value Alterna: 0.896 RNASampler(seed): 0.945 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08		- Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.824 Alterna: 0.671 Sensitivity Mastr(20): 0.761 Alterna: 0.680 Positive Predictive Value Mastr(20): 0.900 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.767 Vsfold4: 0.750 Sensitivity Alterna: 0.777 Vsfold4: 0.725 Positive Predictive Value Alterna: 0.769 Vsfold4: 0.788 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 2.45033651981e-07	+ Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.840 Murlet(seed): 0.656 Sensitivity Alterna: 0.828 Murlet(seed): 0.524 Positive Predictive Value Alterna: 0.860 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.780 MCFold: 0.706 Sensitivity Alterna: 0.789 MCFold: 0.741 Positive Predictive Value Alterna: 0.783 MCFold: 0.689 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.767 Vsfold5: 0.714 Sensitivity Alterna: 0.777 Vsfold5: 0.705 Positive Predictive Value Alterna: 0.769 Vsfold5: 0.737 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.684 RNAwolf: 0.678 Sensitivity Alterna: 0.705 RNAwolf: 0.674 Positive Predictive Value Alterna: 0.679 RNAwolf: 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00114602237498	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.756 NanoFolder: 0.610 Sensitivity Alterna: 0.753 NanoFolder: 0.706 Positive Predictive Value Alterna: 0.771 NanoFolder: 0.545 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.768 RDfolder: 0.690 Sensitivity Alterna: 0.777 RDfolder: 0.652 Positive Predictive Value Alterna: 0.771 RDfolder: 0.745 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: 0.757 RSpredict(seed): 0.502 Sensitivity Alterna: 0.765 RSpredict(seed): 0.350 Positive Predictive Value Alterna: 0.760 RSpredict(seed): 0.739 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.702 Multilign(seed): 0.668 Sensitivity Alterna: 0.685 Multilign(seed): 0.629 Positive Predictive Value Alterna: 0.735 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.671 PPfold(seed): 0.185 Sensitivity Alterna: 0.677 PPfold(seed): 0.047 Positive Predictive Value Alterna: 0.677 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.840 Carnac(seed): 0.420 Sensitivity Alterna: 0.828 Carnac(seed): 0.180 Positive Predictive Value Alterna: 0.860 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.757 Mastr(seed): 0.421 Sensitivity Alterna: 0.765 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.760 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(20)	39 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Mastr(20): 0.610 Sensitivity CentroidAlifold(20): 0.728 Mastr(20): 0.475 Positive Predictive Value CentroidAlifold(20): 0.901 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.887 Mastr(20): 0.577 Sensitivity PETfold_pre2.0(seed): 0.858 Mastr(20): 0.471 Positive Predictive Value PETfold_pre2.0(seed): 0.919 Mastr(20): 0.715 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	11 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.781 Mastr(20): 0.561 Sensitivity ContextFold: 0.731 Mastr(20): 0.430 Positive Predictive Value ContextFold: 0.840 Mastr(20): 0.741 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	33 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.775 Mastr(20): 0.618 Sensitivity MXScarna(seed): 0.732 Mastr(20): 0.469 Positive Predictive Value MXScarna(seed): 0.825 Mastr(20): 0.821 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.790 Mastr(20): 0.620 Sensitivity RNAalifold(20): 0.704 Mastr(20): 0.473 Positive Predictive Value RNAalifold(20): 0.891 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Mastr(20): 0.577 Sensitivity PETfold_pre2.0(20): 0.776 Mastr(20): 0.471 Positive Predictive Value PETfold_pre2.0(20): 0.815 Mastr(20): 0.715 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	15 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.812 Mastr(20): 0.631 Sensitivity PPfold(20): 0.753 Mastr(20): 0.509 Positive Predictive Value PPfold(20): 0.880 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	14 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.712 Mastr(20): 0.616 Sensitivity IPknot: 0.678 Mastr(20): 0.493 Positive Predictive Value IPknot: 0.756 Mastr(20): 0.779 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	34 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.755 Mastr(20): 0.620 Sensitivity MXScarna(20): 0.720 Mastr(20): 0.473 Positive Predictive Value MXScarna(20): 0.796 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.751 Mastr(20): 0.620 Sensitivity RNASampler(20): 0.663 Mastr(20): 0.473 Positive Predictive Value RNASampler(20): 0.856 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.773 Mastr(20): 0.631 Sensitivity TurboFold(20): 0.737 Mastr(20): 0.509 Positive Predictive Value TurboFold(20): 0.817 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.14531876181e-08	39 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 Mastr(20): 0.610 Sensitivity CentroidAlifold(seed): 0.528 Mastr(20): 0.475 Positive Predictive Value CentroidAlifold(seed): 0.921 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.690 Mastr(20): 0.610 Sensitivity CentroidFold: 0.689 Mastr(20): 0.475 Positive Predictive Value CentroidFold: 0.698 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.707 Mastr(20): 0.620 Sensitivity Sfold: 0.683 Mastr(20): 0.473 Positive Predictive Value Sfold: 0.736 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 Mastr(20): 0.657 Sensitivity CentroidHomfold‑LAST: 0.744 Mastr(20): 0.553 Positive Predictive Value CentroidHomfold‑LAST: 0.783 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	34 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.664 Mastr(20): 0.620 Sensitivity Contrafold: 0.681 Mastr(20): 0.473 Positive Predictive Value Contrafold: 0.654 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	20 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.672 Mastr(20): 0.462 Sensitivity RNAalifold(seed): 0.488 Mastr(20): 0.278 Positive Predictive Value RNAalifold(seed): 0.931 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	32 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.690 Mastr(20): 0.612 Sensitivity MaxExpect: 0.693 Mastr(20): 0.463 Positive Predictive Value MaxExpect: 0.694 Mastr(20): 0.817 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	34 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.668 Mastr(20): 0.620 Sensitivity HotKnots: 0.692 Mastr(20): 0.473 Positive Predictive Value HotKnots: 0.651 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.692 Mastr(20): 0.620 Sensitivity UNAFold: 0.701 Mastr(20): 0.473 Positive Predictive Value UNAFold: 0.689 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.679 Mastr(20): 0.573 Sensitivity ProbKnot: 0.700 Mastr(20): 0.412 Positive Predictive Value ProbKnot: 0.664 Mastr(20): 0.804 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	34 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.693 Mastr(20): 0.620 Sensitivity Murlet(20): 0.594 Mastr(20): 0.473 Positive Predictive Value Murlet(20): 0.815 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.687 Mastr(20): 0.620 Sensitivity PknotsRG: 0.709 Mastr(20): 0.473 Positive Predictive Value PknotsRG: 0.673 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.677 Mastr(20): 0.620 Sensitivity RNAfold: 0.694 Mastr(20): 0.473 Positive Predictive Value RNAfold: 0.667 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.685 Mastr(20): 0.620 Sensitivity RNAshapes: 0.694 Mastr(20): 0.473 Positive Predictive Value RNAshapes: 0.682 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.694 Mastr(20): 0.573 Sensitivity Fold: 0.715 Mastr(20): 0.412 Positive Predictive Value Fold: 0.680 Mastr(20): 0.804 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.683 Mastr(20): 0.626 Sensitivity TurboFold(seed): 0.653 Mastr(20): 0.477 Positive Predictive Value TurboFold(seed): 0.723 Mastr(20): 0.831 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	20 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.664 Afold: 0.639 Sensitivity Mastr(20): 0.507 Afold: 0.658 Positive Predictive Value Mastr(20): 0.876 Afold: 0.626 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.71949088499e-07	34 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.686 Mastr(20): 0.620 Sensitivity Carnac(20): 0.518 Mastr(20): 0.473 Positive Predictive Value Carnac(20): 0.915 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.660 Mastr(20): 0.626 Sensitivity RSpredict(20): 0.597 Mastr(20): 0.487 Positive Predictive Value RSpredict(20): 0.735 Mastr(20): 0.812 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 5.6410608252e-08	34 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.660 Mastr(20): 0.620 Sensitivity RNAsubopt: 0.684 Mastr(20): 0.473 Positive Predictive Value RNAsubopt: 0.643 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.97386617324e-07	19 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.715 Mastr(20): 0.646 Sensitivity Cylofold: 0.713 Mastr(20): 0.508 Positive Predictive Value Cylofold: 0.725 Mastr(20): 0.829 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.58287649515e-08	34 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.641 Mastr(20): 0.620 Sensitivity McQFold: 0.648 Mastr(20): 0.473 Positive Predictive Value McQFold: 0.641 Mastr(20): 0.819 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 6.70530687003e-06	11 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.635 Mastr(20): 0.561 Sensitivity RNASLOpt: 0.616 Mastr(20): 0.430 Positive Predictive Value RNASLOpt: 0.662 Mastr(20): 0.741 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	33 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.655 Pknots: 0.619 Sensitivity Mastr(20): 0.529 Pknots: 0.663 Positive Predictive Value Mastr(20): 0.819 Pknots: 0.587 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.83792096436e-08	7 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Mastr(20): 0.649 Sensitivity CRWrnafold: 0.683 Mastr(20): 0.524 Positive Predictive Value CRWrnafold: 0.663 Mastr(20): 0.811 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.652 Mastr(20): 0.639 Sensitivity Multilign(20): 0.624 Mastr(20): 0.520 Positive Predictive Value Multilign(20): 0.692 Mastr(20): 0.796 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000114247382482	9 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.670 Mastr(20): 0.623 Sensitivity RNASampler(seed): 0.604 Mastr(20): 0.439 Positive Predictive Value RNASampler(seed): 0.748 Mastr(20): 0.891 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	13 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.824 Alterna: 0.671 Sensitivity Mastr(20): 0.761 Alterna: 0.680 Positive Predictive Value Mastr(20): 0.900 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08		+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.630 Vsfold4: 0.561 Sensitivity Mastr(20): 0.489 Vsfold4: 0.556 Positive Predictive Value Mastr(20): 0.819 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.557 Mastr(20): 0.507 Sensitivity Murlet(seed): 0.355 Mastr(20): 0.336 Positive Predictive Value Murlet(seed): 0.880 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.692 MCFold: 0.499 Sensitivity Mastr(20): 0.562 MCFold: 0.560 Positive Predictive Value Mastr(20): 0.858 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.630 Vsfold5: 0.494 Sensitivity Mastr(20): 0.489 Vsfold5: 0.496 Positive Predictive Value Mastr(20): 0.819 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.612 RNAwolf: 0.438 Sensitivity Mastr(20): 0.509 RNAwolf: 0.454 Positive Predictive Value Mastr(20): 0.744 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	? Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): 0.669 CMfinder(20): 0.652 Sensitivity Mastr(20): 0.570 CMfinder(20): 0.518 Positive Predictive Value Mastr(20): 0.793 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.595 NanoFolder: 0.329 Sensitivity Mastr(20): 0.511 NanoFolder: 0.405 Positive Predictive Value Mastr(20): 0.703 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.777 RDfolder: 0.636 Sensitivity Mastr(20): 0.693 RDfolder: 0.602 Positive Predictive Value Mastr(20): 0.880 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.626 RSpredict(seed): 0.230 Sensitivity Mastr(20): 0.487 RSpredict(seed): 0.114 Positive Predictive Value Mastr(20): 0.812 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Mastr(20): 0.616 Sensitivity Multilign(seed): 0.682 Mastr(20): 0.488 Positive Predictive Value Multilign(seed): 0.793 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.616 PPfold(seed): 0.046 Sensitivity Mastr(20): 0.493 PPfold(seed): 0.009 Positive Predictive Value Mastr(20): 0.779 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.604 Carnac(seed): 0.220 Sensitivity Mastr(20): 0.449 Carnac(seed): 0.049 Positive Predictive Value Mastr(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.620 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.473 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.819 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Mastr(20): 0.274 Sensitivity PETfold_2.0(seed): 0.889 Mastr(20): 0.259 Positive Predictive Value PETfold_2.0(seed): 0.923 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Mastr(20): 0.274 Sensitivity PETfold_2.0(20): 0.889 Mastr(20): 0.259 Positive Predictive Value PETfold_2.0(20): 0.923 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Vsfold4	38 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.817 Vsfold4: 0.526 Sensitivity CentroidAlifold(20): 0.740 Vsfold4: 0.525 Positive Predictive Value CentroidAlifold(20): 0.906 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.878 Vsfold4: 0.538 Sensitivity PETfold_pre2.0(seed): 0.842 Vsfold4: 0.533 Positive Predictive Value PETfold_pre2.0(seed): 0.918 Vsfold4: 0.554 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	41 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.773 Vsfold4: 0.583 Sensitivity ContextFold: 0.750 Vsfold4: 0.572 Positive Predictive Value ContextFold: 0.803 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.779 Vsfold4: 0.613 Sensitivity MXScarna(seed): 0.738 Vsfold4: 0.610 Positive Predictive Value MXScarna(seed): 0.826 Vsfold4: 0.623 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.802 Vsfold4: 0.561 Sensitivity RNAalifold(20): 0.714 Vsfold4: 0.556 Positive Predictive Value RNAalifold(20): 0.904 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Vsfold4: 0.506 Sensitivity PETfold_pre2.0(20): 0.814 Vsfold4: 0.507 Positive Predictive Value PETfold_pre2.0(20): 0.847 Vsfold4: 0.515 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	14 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.844 Vsfold4: 0.619 Sensitivity PPfold(20): 0.791 Vsfold4: 0.603 Positive Predictive Value PPfold(20): 0.906 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	49 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.764 Vsfold4: 0.590 Sensitivity IPknot: 0.751 Vsfold4: 0.580 Positive Predictive Value IPknot: 0.783 Vsfold4: 0.611 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.767 Vsfold4: 0.561 Sensitivity MXScarna(20): 0.734 Vsfold4: 0.556 Positive Predictive Value MXScarna(20): 0.807 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold4: 0.561 Sensitivity RNASampler(20): 0.675 Vsfold4: 0.556 Positive Predictive Value RNASampler(20): 0.872 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.796 Vsfold4: 0.619 Sensitivity TurboFold(20): 0.762 Vsfold4: 0.603 Positive Predictive Value TurboFold(20): 0.838 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.45096400029e-08	57 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.681 Vsfold4: 0.582 Sensitivity CentroidAlifold(seed): 0.529 Vsfold4: 0.582 Positive Predictive Value CentroidAlifold(seed): 0.882 Vsfold4: 0.590 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.747 Vsfold4: 0.610 Sensitivity CentroidFold: 0.747 Vsfold4: 0.601 Positive Predictive Value CentroidFold: 0.753 Vsfold4: 0.628 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.761 Vsfold4: 0.635 Sensitivity Sfold: 0.753 Vsfold4: 0.625 Positive Predictive Value Sfold: 0.775 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.740 Vsfold4: 0.604 Sensitivity CentroidHomfold‑LAST: 0.667 Vsfold4: 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.828 Vsfold4: 0.629 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.753 Vsfold4: 0.635 Sensitivity Contrafold: 0.770 Vsfold4: 0.625 Positive Predictive Value Contrafold: 0.742 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.682 Vsfold4: 0.574 Sensitivity RNAalifold(seed): 0.530 Vsfold4: 0.575 Positive Predictive Value RNAalifold(seed): 0.883 Vsfold4: 0.581 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	109 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.741 Vsfold4: 0.627 Sensitivity MaxExpect: 0.754 Vsfold4: 0.619 Positive Predictive Value MaxExpect: 0.734 Vsfold4: 0.646 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.752 Vsfold4: 0.635 Sensitivity HotKnots: 0.774 Vsfold4: 0.625 Positive Predictive Value HotKnots: 0.738 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.753 Vsfold4: 0.635 Sensitivity UNAFold: 0.766 Vsfold4: 0.625 Positive Predictive Value UNAFold: 0.747 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	85 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.727 Vsfold4: 0.607 Sensitivity ProbKnot: 0.758 Vsfold4: 0.600 Positive Predictive Value ProbKnot: 0.703 Vsfold4: 0.622 Number of pairs reference - predicted secondary structure: 85 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.703 Vsfold4: 0.561 Sensitivity Murlet(20): 0.601 Vsfold4: 0.556 Positive Predictive Value Murlet(20): 0.827 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.735 Vsfold4: 0.635 Sensitivity PknotsRG: 0.757 Vsfold4: 0.625 Positive Predictive Value PknotsRG: 0.720 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.742 Vsfold4: 0.635 Sensitivity RNAfold: 0.760 Vsfold4: 0.625 Positive Predictive Value RNAfold: 0.732 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.731 Vsfold4: 0.635 Sensitivity RNAshapes: 0.744 Vsfold4: 0.625 Positive Predictive Value RNAshapes: 0.725 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	93 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.758 Vsfold4: 0.629 Sensitivity Fold: 0.780 Vsfold4: 0.622 Positive Predictive Value Fold: 0.743 Vsfold4: 0.645 Number of pairs reference - predicted secondary structure: 93 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold4: 0.487 Sensitivity TurboFold(seed): 0.624 Vsfold4: 0.468 Positive Predictive Value TurboFold(seed): 0.688 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	98 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.725 Vsfold4: 0.638 Sensitivity Afold: 0.752 Vsfold4: 0.630 Positive Predictive Value Afold: 0.706 Vsfold4: 0.655 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.695 Vsfold4: 0.561 Sensitivity Carnac(20): 0.528 Vsfold4: 0.556 Positive Predictive Value Carnac(20): 0.920 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.669 Vsfold4: 0.540 Sensitivity RSpredict(20): 0.606 Vsfold4: 0.539 Positive Predictive Value RSpredict(20): 0.746 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.723 Vsfold4: 0.635 Sensitivity RNAsubopt: 0.744 Vsfold4: 0.625 Positive Predictive Value RNAsubopt: 0.709 Vsfold4: 0.653 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.708 Vsfold4: 0.652 Sensitivity Cylofold: 0.697 Vsfold4: 0.637 Positive Predictive Value Cylofold: 0.729 Vsfold4: 0.678 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	128 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.697 Vsfold4: 0.632 Sensitivity McQFold: 0.698 Vsfold4: 0.623 Positive Predictive Value McQFold: 0.703 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.645 Vsfold4: 0.583 Sensitivity RNASLOpt: 0.608 Vsfold4: 0.572 Positive Predictive Value RNASLOpt: 0.694 Vsfold4: 0.606 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	125 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.729 Vsfold4: 0.674 Sensitivity Pknots: 0.752 Vsfold4: 0.656 Positive Predictive Value Pknots: 0.717 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.683 Vsfold4: 0.580 Sensitivity CRWrnafold: 0.690 Vsfold4: 0.571 Positive Predictive Value CRWrnafold: 0.689 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.652 Vsfold4: 0.563 Sensitivity Multilign(20): 0.624 Vsfold4: 0.547 Positive Predictive Value Multilign(20): 0.692 Vsfold4: 0.592 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	18 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.752 Vsfold4: 0.688 Sensitivity RNASampler(seed): 0.659 Vsfold4: 0.675 Positive Predictive Value RNASampler(seed): 0.865 Vsfold4: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	89 Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.767 Vsfold4: 0.750 Sensitivity Alterna: 0.777 Vsfold4: 0.725 Positive Predictive Value Alterna: 0.769 Vsfold4: 0.788 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 2.45033651981e-07	33 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.630 Vsfold4: 0.561 Sensitivity Mastr(20): 0.489 Vsfold4: 0.556 Positive Predictive Value Mastr(20): 0.819 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.626 Murlet(seed): 0.595 Sensitivity Vsfold4: 0.609 Murlet(seed): 0.422 Positive Predictive Value Vsfold4: 0.654 Murlet(seed): 0.850 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.652 MCFold: 0.639 Sensitivity Vsfold4: 0.636 MCFold: 0.677 Positive Predictive Value Vsfold4: 0.680 MCFold: 0.615 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.638 Vsfold5: 0.598 Sensitivity Vsfold4: 0.630 Vsfold5: 0.600 Positive Predictive Value Vsfold4: 0.657 Vsfold5: 0.605 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.550 RNAwolf: 0.524 Sensitivity Vsfold4: 0.542 RNAwolf: 0.530 Positive Predictive Value Vsfold4: 0.569 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.721 CMfinder(20): 0.652 Sensitivity Vsfold4: 0.702 CMfinder(20): 0.518 Positive Predictive Value Vsfold4: 0.748 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.571 NanoFolder: 0.394 Sensitivity Vsfold4: 0.570 NanoFolder: 0.485 Positive Predictive Value Vsfold4: 0.583 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.751 RDfolder: 0.677 Sensitivity Vsfold4: 0.724 RDfolder: 0.637 Positive Predictive Value Vsfold4: 0.791 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.592 RSpredict(seed): 0.318 Sensitivity Vsfold4: 0.592 RSpredict(seed): 0.181 Positive Predictive Value Vsfold4: 0.599 RSpredict(seed): 0.573 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.737 Vsfold4: 0.555 Sensitivity Multilign(seed): 0.689 Vsfold4: 0.530 Positive Predictive Value Multilign(seed): 0.800 Vsfold4: 0.602 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.610 PPfold(seed): 0.094 Sensitivity Vsfold4: 0.593 PPfold(seed): 0.017 Positive Predictive Value Vsfold4: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.616 Carnac(seed): 0.287 Sensitivity Vsfold4: 0.601 Carnac(seed): 0.084 Positive Predictive Value Vsfold4: 0.642 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.608 Mastr(seed): 0.285 Sensitivity Vsfold4: 0.607 Mastr(seed): 0.092 Positive Predictive Value Vsfold4: 0.617 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Vsfold4: 0.193 Sensitivity PETfold_2.0(seed): 0.889 Vsfold4: 0.185 Positive Predictive Value PETfold_2.0(seed): 0.923 Vsfold4: 0.217 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Vsfold4: 0.193 Sensitivity PETfold_2.0(20): 0.889 Vsfold4: 0.185 Positive Predictive Value PETfold_2.0(20): 0.923 Vsfold4: 0.217 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Murlet(seed)	20 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.722 Murlet(seed): 0.554 Sensitivity CentroidAlifold(20): 0.602 Murlet(seed): 0.350 Positive Predictive Value CentroidAlifold(20): 0.870 Murlet(seed): 0.884 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	13 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Murlet(seed): 0.473 Sensitivity PETfold_pre2.0(seed): 0.697 Murlet(seed): 0.300 Positive Predictive Value PETfold_pre2.0(seed): 0.853 Murlet(seed): 0.756 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	9 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.605 Murlet(seed): 0.470 Sensitivity ContextFold: 0.559 Murlet(seed): 0.313 Positive Predictive Value ContextFold: 0.663 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	30 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.735 Murlet(seed): 0.594 Sensitivity MXScarna(seed): 0.689 Murlet(seed): 0.418 Positive Predictive Value MXScarna(seed): 0.792 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.701 Murlet(seed): 0.557 Sensitivity RNAalifold(20): 0.603 Murlet(seed): 0.355 Positive Predictive Value RNAalifold(20): 0.821 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	8 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.547 Murlet(seed): 0.515 Sensitivity PETfold_pre2.0(20): 0.518 Murlet(seed): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.585 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.681 Murlet(seed): 0.543 Sensitivity PPfold(20): 0.596 Murlet(seed): 0.360 Positive Predictive Value PPfold(20): 0.786 Murlet(seed): 0.830 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.670 Murlet(seed): 0.496 Sensitivity IPknot: 0.610 Murlet(seed): 0.337 Positive Predictive Value IPknot: 0.745 Murlet(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.4651262096e-08	19 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.711 Murlet(seed): 0.557 Sensitivity MXScarna(20): 0.667 Murlet(seed): 0.355 Positive Predictive Value MXScarna(20): 0.764 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.50323628132e-08	19 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.701 Murlet(seed): 0.557 Sensitivity RNASampler(20): 0.610 Murlet(seed): 0.355 Positive Predictive Value RNASampler(20): 0.813 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	9 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.691 Murlet(seed): 0.543 Sensitivity TurboFold(20): 0.645 Murlet(seed): 0.360 Positive Predictive Value TurboFold(20): 0.749 Murlet(seed): 0.830 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	33 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 Murlet(seed): 0.584 Sensitivity CentroidAlifold(seed): 0.682 Murlet(seed): 0.402 Positive Predictive Value CentroidAlifold(seed): 0.891 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.758 Murlet(seed): 0.584 Sensitivity CentroidFold: 0.736 Murlet(seed): 0.402 Positive Predictive Value CentroidFold: 0.788 Murlet(seed): 0.856 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.759 Murlet(seed): 0.594 Sensitivity Sfold: 0.723 Murlet(seed): 0.418 Positive Predictive Value Sfold: 0.803 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Murlet(seed): 0.503 Sensitivity CentroidHomfold‑LAST: 0.617 Murlet(seed): 0.352 Positive Predictive Value CentroidHomfold‑LAST: 0.672 Murlet(seed): 0.736 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	30 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.750 Murlet(seed): 0.594 Sensitivity Contrafold: 0.750 Murlet(seed): 0.418 Positive Predictive Value Contrafold: 0.758 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.733 Murlet(seed): 0.594 Sensitivity RNAalifold(seed): 0.591 Murlet(seed): 0.418 Positive Predictive Value RNAalifold(seed): 0.916 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.708 Murlet(seed): 0.593 Sensitivity MaxExpect: 0.705 Murlet(seed): 0.420 Positive Predictive Value MaxExpect: 0.720 Murlet(seed): 0.848 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.710 Murlet(seed): 0.594 Sensitivity HotKnots: 0.730 Murlet(seed): 0.418 Positive Predictive Value HotKnots: 0.699 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.712 Murlet(seed): 0.594 Sensitivity UNAFold: 0.716 Murlet(seed): 0.418 Positive Predictive Value UNAFold: 0.717 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.633 Murlet(seed): 0.544 Sensitivity ProbKnot: 0.653 Murlet(seed): 0.362 Positive Predictive Value ProbKnot: 0.622 Murlet(seed): 0.829 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	19 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.620 Murlet(seed): 0.557 Sensitivity Murlet(20): 0.509 Murlet(seed): 0.355 Positive Predictive Value Murlet(20): 0.763 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	30 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.735 Murlet(seed): 0.594 Sensitivity PknotsRG: 0.747 Murlet(seed): 0.418 Positive Predictive Value PknotsRG: 0.730 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.732 Murlet(seed): 0.594 Sensitivity RNAfold: 0.740 Murlet(seed): 0.418 Positive Predictive Value RNAfold: 0.732 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.746 Murlet(seed): 0.594 Sensitivity RNAshapes: 0.750 Murlet(seed): 0.418 Positive Predictive Value RNAshapes: 0.749 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.685 Murlet(seed): 0.582 Sensitivity Fold: 0.704 Murlet(seed): 0.405 Positive Predictive Value Fold: 0.674 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	10 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.611 Murlet(seed): 0.546 Sensitivity TurboFold(seed): 0.578 Murlet(seed): 0.373 Positive Predictive Value TurboFold(seed): 0.657 Murlet(seed): 0.808 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	21 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.771 Murlet(seed): 0.613 Sensitivity Afold: 0.777 Murlet(seed): 0.449 Positive Predictive Value Afold: 0.773 Murlet(seed): 0.848 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.85839946686e-08	19 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.611 Murlet(seed): 0.557 Sensitivity Carnac(20): 0.401 Murlet(seed): 0.355 Positive Predictive Value Carnac(20): 0.938 Murlet(seed): 0.880 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	21 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.554 RSpredict(20): 0.507 Sensitivity Murlet(seed): 0.349 RSpredict(20): 0.445 Positive Predictive Value Murlet(seed): 0.886 RSpredict(20): 0.588 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	30 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.695 Murlet(seed): 0.594 Sensitivity RNAsubopt: 0.709 Murlet(seed): 0.418 Positive Predictive Value RNAsubopt: 0.690 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.652 Murlet(seed): 0.543 Sensitivity Cylofold: 0.633 Murlet(seed): 0.372 Positive Predictive Value Cylofold: 0.683 Murlet(seed): 0.804 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.54914456376e-08	30 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.722 Murlet(seed): 0.594 Sensitivity McQFold: 0.717 Murlet(seed): 0.418 Positive Predictive Value McQFold: 0.735 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.490 Murlet(seed): 0.470 Sensitivity RNASLOpt: 0.474 Murlet(seed): 0.313 Positive Predictive Value RNASLOpt: 0.518 Murlet(seed): 0.717 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	30 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.683 Murlet(seed): 0.594 Sensitivity Pknots: 0.716 Murlet(seed): 0.418 Positive Predictive Value Pknots: 0.661 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.530 Multilign(20): 0.500 Sensitivity Murlet(seed): 0.344 Multilign(20): 0.464 Positive Predictive Value Murlet(seed): 0.828 Multilign(20): 0.554 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Murlet(seed): 0.615 Sensitivity RNASampler(seed): 0.634 Murlet(seed): 0.457 Positive Predictive Value RNASampler(seed): 0.843 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	17 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.840 Murlet(seed): 0.656 Sensitivity Alterna: 0.828 Murlet(seed): 0.524 Positive Predictive Value Alterna: 0.860 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08	19 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.557 Mastr(20): 0.507 Sensitivity Murlet(seed): 0.355 Mastr(20): 0.336 Positive Predictive Value Murlet(seed): 0.880 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	28 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.626 Murlet(seed): 0.595 Sensitivity Vsfold4: 0.609 Murlet(seed): 0.422 Positive Predictive Value Vsfold4: 0.654 Murlet(seed): 0.850 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.6410608252e-08		+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.589 MCFold: 0.559 Sensitivity Murlet(seed): 0.413 MCFold: 0.606 Positive Predictive Value Murlet(seed): 0.848 MCFold: 0.526 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.37177523642e-07	= Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.598 Vsfold5: 0.597 Sensitivity Murlet(seed): 0.425 Vsfold5: 0.591 Positive Predictive Value Murlet(seed): 0.852 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0307664235267	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.493 RNAwolf: 0.418 Sensitivity Murlet(seed): 0.320 RNAwolf: 0.431 Positive Predictive Value Murlet(seed): 0.769 RNAwolf: 0.420 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	? CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.536 Murlet(seed): 0.165 Sensitivity CMfinder(20): 0.292 Murlet(seed): 0.125 Positive Predictive Value CMfinder(20): 1.000 Murlet(seed): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.466 NanoFolder: 0.294 Sensitivity Murlet(seed): 0.313 NanoFolder: 0.357 Positive Predictive Value Murlet(seed): 0.706 NanoFolder: 0.259 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	= Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.642 RDfolder: 0.633 Sensitivity Murlet(seed): 0.494 RDfolder: 0.582 Positive Predictive Value Murlet(seed): 0.850 RDfolder: 0.707 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.00102881663438	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.583 RSpredict(seed): 0.467 Sensitivity Murlet(seed): 0.401 RSpredict(seed): 0.310 Positive Predictive Value Murlet(seed): 0.857 RSpredict(seed): 0.715 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Murlet(seed): 0.516 Sensitivity Multilign(seed): 0.591 Murlet(seed): 0.356 Positive Predictive Value Multilign(seed): 0.724 Murlet(seed): 0.763 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.496 PPfold(seed): 0.124 Sensitivity Murlet(seed): 0.337 PPfold(seed): 0.034 Positive Predictive Value Murlet(seed): 0.742 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.594 Carnac(seed): 0.300 Sensitivity Murlet(seed): 0.418 Carnac(seed): 0.091 Positive Predictive Value Murlet(seed): 0.855 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.594 Mastr(seed): 0.382 Sensitivity Murlet(seed): 0.418 Mastr(seed): 0.165 Positive Predictive Value Murlet(seed): 0.855 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 30 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	? PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 Murlet(seed): 0.475 Sensitivity PETfold_2.0(seed): 0.806 Murlet(seed): 0.258 Positive Predictive Value PETfold_2.0(seed): 0.862 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MCFold	34 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.815 MCFold: 0.494 Sensitivity CentroidAlifold(20): 0.744 MCFold: 0.554 Positive Predictive Value CentroidAlifold(20): 0.896 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.863 MCFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.823 MCFold: 0.524 Positive Predictive Value PETfold_pre2.0(seed): 0.907 MCFold: 0.439 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	50 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.718 MCFold: 0.541 Sensitivity ContextFold: 0.700 MCFold: 0.576 Positive Predictive Value ContextFold: 0.743 MCFold: 0.519 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.776 MCFold: 0.557 Sensitivity MXScarna(seed): 0.736 MCFold: 0.608 Positive Predictive Value MXScarna(seed): 0.824 MCFold: 0.522 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.786 MCFold: 0.499 Sensitivity RNAalifold(20): 0.728 MCFold: 0.560 Positive Predictive Value RNAalifold(20): 0.854 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 MCFold: 0.483 Sensitivity PETfold_pre2.0(20): 0.751 MCFold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.788 MCFold: 0.439 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	19 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.778 MCFold: 0.518 Sensitivity PPfold(20): 0.736 MCFold: 0.574 Positive Predictive Value PPfold(20): 0.828 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.52609899389e-08	58 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.724 MCFold: 0.550 Sensitivity IPknot: 0.713 MCFold: 0.586 Positive Predictive Value IPknot: 0.743 MCFold: 0.528 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.758 MCFold: 0.499 Sensitivity MXScarna(20): 0.735 MCFold: 0.560 Positive Predictive Value MXScarna(20): 0.787 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.754 MCFold: 0.499 Sensitivity RNASampler(20): 0.696 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.823 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.752 MCFold: 0.518 Sensitivity TurboFold(20): 0.747 MCFold: 0.574 Positive Predictive Value TurboFold(20): 0.762 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	50 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.695 MCFold: 0.553 Sensitivity CentroidAlifold(seed): 0.538 MCFold: 0.605 Positive Predictive Value CentroidAlifold(seed): 0.905 MCFold: 0.518 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.765 MCFold: 0.608 Sensitivity CentroidFold: 0.759 MCFold: 0.649 Positive Predictive Value CentroidFold: 0.779 MCFold: 0.582 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.781 MCFold: 0.622 Sensitivity Sfold: 0.770 MCFold: 0.663 Positive Predictive Value Sfold: 0.799 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 MCFold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.696 MCFold: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.785 MCFold: 0.556 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.748 MCFold: 0.622 Sensitivity Contrafold: 0.766 MCFold: 0.663 Positive Predictive Value Contrafold: 0.740 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.703 MCFold: 0.569 Sensitivity RNAalifold(seed): 0.549 MCFold: 0.616 Positive Predictive Value RNAalifold(seed): 0.905 MCFold: 0.536 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	113 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.740 MCFold: 0.599 Sensitivity MaxExpect: 0.751 MCFold: 0.640 Positive Predictive Value MaxExpect: 0.736 MCFold: 0.572 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.760 MCFold: 0.622 Sensitivity HotKnots: 0.785 MCFold: 0.663 Positive Predictive Value HotKnots: 0.743 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.763 MCFold: 0.622 Sensitivity UNAFold: 0.777 MCFold: 0.663 Positive Predictive Value UNAFold: 0.758 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.726 MCFold: 0.604 Sensitivity ProbKnot: 0.753 MCFold: 0.640 Positive Predictive Value ProbKnot: 0.708 MCFold: 0.581 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.717 MCFold: 0.499 Sensitivity Murlet(20): 0.639 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.810 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	131 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.757 MCFold: 0.622 Sensitivity PknotsRG: 0.781 MCFold: 0.663 Positive Predictive Value PknotsRG: 0.742 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.758 MCFold: 0.622 Sensitivity RNAfold: 0.775 MCFold: 0.663 Positive Predictive Value RNAfold: 0.749 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.756 MCFold: 0.622 Sensitivity RNAshapes: 0.768 MCFold: 0.663 Positive Predictive Value RNAshapes: 0.753 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.746 MCFold: 0.621 Sensitivity Fold: 0.770 MCFold: 0.656 Positive Predictive Value Fold: 0.731 MCFold: 0.599 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.618 MCFold: 0.470 Sensitivity TurboFold(seed): 0.612 MCFold: 0.519 Positive Predictive Value TurboFold(seed): 0.633 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	96 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.768 MCFold: 0.680 Sensitivity Afold: 0.790 MCFold: 0.725 Positive Predictive Value Afold: 0.755 MCFold: 0.650 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.717 MCFold: 0.499 Sensitivity Carnac(20): 0.561 MCFold: 0.560 Positive Predictive Value Carnac(20): 0.922 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.691 MCFold: 0.499 Sensitivity RSpredict(20): 0.644 MCFold: 0.560 Positive Predictive Value RSpredict(20): 0.749 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.734 MCFold: 0.622 Sensitivity RNAsubopt: 0.757 MCFold: 0.663 Positive Predictive Value RNAsubopt: 0.721 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.739 MCFold: 0.631 Sensitivity Cylofold: 0.720 MCFold: 0.665 Positive Predictive Value Cylofold: 0.767 MCFold: 0.612 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	130 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.713 MCFold: 0.620 Sensitivity McQFold: 0.710 MCFold: 0.660 Positive Predictive Value McQFold: 0.725 MCFold: 0.594 Number of pairs reference - predicted secondary structure: 130 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.593 MCFold: 0.541 Sensitivity RNASLOpt: 0.571 MCFold: 0.576 Positive Predictive Value RNASLOpt: 0.626 MCFold: 0.519 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.691 MCFold: 0.622 Sensitivity Pknots: 0.723 MCFold: 0.663 Positive Predictive Value Pknots: 0.671 MCFold: 0.597 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.682 MCFold: 0.639 Sensitivity CRWrnafold: 0.690 MCFold: 0.670 Positive Predictive Value CRWrnafold: 0.685 MCFold: 0.621 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.611 MCFold: 0.512 Sensitivity Multilign(20): 0.597 MCFold: 0.565 Positive Predictive Value Multilign(20): 0.633 MCFold: 0.475 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.39162260866e-08	21 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.696 MCFold: 0.616 Sensitivity RNASampler(seed): 0.620 MCFold: 0.681 Positive Predictive Value RNASampler(seed): 0.788 MCFold: 0.565 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	86 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.780 MCFold: 0.706 Sensitivity Alterna: 0.789 MCFold: 0.741 Positive Predictive Value Alterna: 0.783 MCFold: 0.689 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.692 MCFold: 0.499 Sensitivity Mastr(20): 0.562 MCFold: 0.560 Positive Predictive Value Mastr(20): 0.858 MCFold: 0.456 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.652 MCFold: 0.639 Sensitivity Vsfold4: 0.636 MCFold: 0.677 Positive Predictive Value Vsfold4: 0.680 MCFold: 0.615 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.589 MCFold: 0.559 Sensitivity Murlet(seed): 0.413 MCFold: 0.606 Positive Predictive Value Murlet(seed): 0.848 MCFold: 0.526 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.37177523642e-07		+ MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.638 Vsfold5: 0.629 Sensitivity MCFold: 0.682 Vsfold5: 0.628 Positive Predictive Value MCFold: 0.610 Vsfold5: 0.642 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 2.29562105844e-05	+ MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.550 RNAwolf: 0.495 Sensitivity MCFold: 0.586 RNAwolf: 0.501 Positive Predictive Value MCFold: 0.528 RNAwolf: 0.503 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.660 MCFold: 0.477 Sensitivity CMfinder(20): 0.580 MCFold: 0.543 Positive Predictive Value CMfinder(20): 0.759 MCFold: 0.429 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.574 NanoFolder: 0.440 Sensitivity MCFold: 0.606 NanoFolder: 0.545 Positive Predictive Value MCFold: 0.554 NanoFolder: 0.369 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.705 MCFold: 0.698 Sensitivity RDfolder: 0.659 MCFold: 0.733 Positive Predictive Value RDfolder: 0.769 MCFold: 0.680 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 0.0133909664952	+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.557 RSpredict(seed): 0.331 Sensitivity MCFold: 0.608 RSpredict(seed): 0.191 Positive Predictive Value MCFold: 0.521 RSpredict(seed): 0.591 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.574 MCFold: 0.476 Sensitivity Multilign(seed): 0.524 MCFold: 0.508 Positive Predictive Value Multilign(seed): 0.638 MCFold: 0.459 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.489 PPfold(seed): 0.175 Sensitivity MCFold: 0.538 PPfold(seed): 0.050 Positive Predictive Value MCFold: 0.456 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.571 Carnac(seed): 0.324 Sensitivity MCFold: 0.622 Carnac(seed): 0.106 Positive Predictive Value MCFold: 0.535 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.557 Mastr(seed): 0.297 Sensitivity MCFold: 0.608 Mastr(seed): 0.103 Positive Predictive Value MCFold: 0.521 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Vsfold5	38 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.817 Vsfold5: 0.480 Sensitivity CentroidAlifold(20): 0.740 Vsfold5: 0.486 Positive Predictive Value CentroidAlifold(20): 0.906 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.876 Vsfold5: 0.481 Sensitivity PETfold_pre2.0(seed): 0.839 Vsfold5: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.916 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	39 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.784 Vsfold5: 0.507 Sensitivity ContextFold: 0.759 Vsfold5: 0.514 Positive Predictive Value ContextFold: 0.816 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.777 Vsfold5: 0.567 Sensitivity MXScarna(seed): 0.737 Vsfold5: 0.569 Positive Predictive Value MXScarna(seed): 0.824 Vsfold5: 0.574 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.802 Vsfold5: 0.494 Sensitivity RNAalifold(20): 0.714 Vsfold5: 0.496 Positive Predictive Value RNAalifold(20): 0.904 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Vsfold5: 0.451 Sensitivity PETfold_pre2.0(20): 0.814 Vsfold5: 0.468 Positive Predictive Value PETfold_pre2.0(20): 0.847 Vsfold5: 0.447 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	14 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.844 Vsfold5: 0.546 Sensitivity PPfold(20): 0.791 Vsfold5: 0.544 Positive Predictive Value PPfold(20): 0.906 Vsfold5: 0.561 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	47 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.753 Vsfold5: 0.523 Sensitivity IPknot: 0.737 Vsfold5: 0.531 Positive Predictive Value IPknot: 0.777 Vsfold5: 0.529 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.767 Vsfold5: 0.494 Sensitivity MXScarna(20): 0.734 Vsfold5: 0.496 Positive Predictive Value MXScarna(20): 0.807 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold5: 0.494 Sensitivity RNASampler(20): 0.675 Vsfold5: 0.496 Positive Predictive Value RNASampler(20): 0.872 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.796 Vsfold5: 0.546 Sensitivity TurboFold(20): 0.762 Vsfold5: 0.544 Positive Predictive Value TurboFold(20): 0.838 Vsfold5: 0.561 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	58 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 Vsfold5: 0.548 Sensitivity CentroidAlifold(seed): 0.533 Vsfold5: 0.556 Positive Predictive Value CentroidAlifold(seed): 0.883 Vsfold5: 0.549 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	124 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.752 Vsfold5: 0.572 Sensitivity CentroidFold: 0.751 Vsfold5: 0.576 Positive Predictive Value CentroidFold: 0.758 Vsfold5: 0.578 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.754 Vsfold5: 0.593 Sensitivity Sfold: 0.745 Vsfold5: 0.595 Positive Predictive Value Sfold: 0.770 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.706 Vsfold5: 0.531 Sensitivity CentroidHomfold‑LAST: 0.642 Vsfold5: 0.538 Positive Predictive Value CentroidHomfold‑LAST: 0.786 Vsfold5: 0.539 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.759 Vsfold5: 0.593 Sensitivity Contrafold: 0.776 Vsfold5: 0.595 Positive Predictive Value Contrafold: 0.750 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.686 Vsfold5: 0.550 Sensitivity RNAalifold(seed): 0.535 Vsfold5: 0.552 Positive Predictive Value RNAalifold(seed): 0.884 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	107 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.731 Vsfold5: 0.578 Sensitivity MaxExpect: 0.744 Vsfold5: 0.579 Positive Predictive Value MaxExpect: 0.725 Vsfold5: 0.588 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.747 Vsfold5: 0.593 Sensitivity HotKnots: 0.768 Vsfold5: 0.595 Positive Predictive Value HotKnots: 0.732 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.745 Vsfold5: 0.593 Sensitivity UNAFold: 0.758 Vsfold5: 0.595 Positive Predictive Value UNAFold: 0.738 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	83 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.715 Vsfold5: 0.565 Sensitivity ProbKnot: 0.746 Vsfold5: 0.570 Positive Predictive Value ProbKnot: 0.691 Vsfold5: 0.570 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.703 Vsfold5: 0.494 Sensitivity Murlet(20): 0.601 Vsfold5: 0.496 Positive Predictive Value Murlet(20): 0.827 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.732 Vsfold5: 0.593 Sensitivity PknotsRG: 0.754 Vsfold5: 0.595 Positive Predictive Value PknotsRG: 0.717 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.737 Vsfold5: 0.593 Sensitivity RNAfold: 0.754 Vsfold5: 0.595 Positive Predictive Value RNAfold: 0.726 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.729 Vsfold5: 0.593 Sensitivity RNAshapes: 0.742 Vsfold5: 0.595 Positive Predictive Value RNAshapes: 0.724 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.747 Vsfold5: 0.586 Sensitivity Fold: 0.769 Vsfold5: 0.589 Positive Predictive Value Fold: 0.731 Vsfold5: 0.594 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.666 Vsfold5: 0.438 Sensitivity TurboFold(seed): 0.635 Vsfold5: 0.438 Positive Predictive Value TurboFold(seed): 0.708 Vsfold5: 0.455 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	96 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.723 Vsfold5: 0.599 Sensitivity Afold: 0.750 Vsfold5: 0.600 Positive Predictive Value Afold: 0.704 Vsfold5: 0.607 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.695 Vsfold5: 0.494 Sensitivity Carnac(20): 0.528 Vsfold5: 0.496 Positive Predictive Value Carnac(20): 0.920 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.669 Vsfold5: 0.493 Sensitivity RSpredict(20): 0.606 Vsfold5: 0.499 Positive Predictive Value RSpredict(20): 0.746 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.722 Vsfold5: 0.593 Sensitivity RNAsubopt: 0.743 Vsfold5: 0.595 Positive Predictive Value RNAsubopt: 0.709 Vsfold5: 0.601 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.699 Vsfold5: 0.592 Sensitivity Cylofold: 0.685 Vsfold5: 0.592 Positive Predictive Value Cylofold: 0.723 Vsfold5: 0.604 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.703 Vsfold5: 0.590 Sensitivity McQFold: 0.702 Vsfold5: 0.592 Positive Predictive Value McQFold: 0.712 Vsfold5: 0.598 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.641 Vsfold5: 0.507 Sensitivity RNASLOpt: 0.622 Vsfold5: 0.514 Positive Predictive Value RNASLOpt: 0.671 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.732 Vsfold5: 0.629 Sensitivity Pknots: 0.753 Vsfold5: 0.626 Positive Predictive Value Pknots: 0.721 Vsfold5: 0.645 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.678 Vsfold5: 0.525 Sensitivity CRWrnafold: 0.685 Vsfold5: 0.528 Positive Predictive Value CRWrnafold: 0.683 Vsfold5: 0.538 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.652 Vsfold5: 0.495 Sensitivity Multilign(20): 0.624 Vsfold5: 0.493 Positive Predictive Value Multilign(20): 0.692 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	18 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.752 Vsfold5: 0.732 Sensitivity RNASampler(seed): 0.659 Vsfold5: 0.733 Positive Predictive Value RNASampler(seed): 0.865 Vsfold5: 0.739 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48421610739e-06	89 Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.767 Vsfold5: 0.714 Sensitivity Alterna: 0.777 Vsfold5: 0.705 Positive Predictive Value Alterna: 0.769 Vsfold5: 0.737 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.630 Vsfold5: 0.494 Sensitivity Mastr(20): 0.489 Vsfold5: 0.496 Positive Predictive Value Mastr(20): 0.819 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.638 Vsfold5: 0.598 Sensitivity Vsfold4: 0.630 Vsfold5: 0.600 Positive Predictive Value Vsfold4: 0.657 Vsfold5: 0.605 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.598 Vsfold5: 0.597 Sensitivity Murlet(seed): 0.425 Vsfold5: 0.591 Positive Predictive Value Murlet(seed): 0.852 Vsfold5: 0.615 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 0.0307664235267	124 MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.638 Vsfold5: 0.629 Sensitivity MCFold: 0.682 Vsfold5: 0.628 Positive Predictive Value MCFold: 0.610 Vsfold5: 0.642 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 2.29562105844e-05		- RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold5: 0.505 Sensitivity RNAwolf: 0.524 Vsfold5: 0.518 Positive Predictive Value RNAwolf: 0.526 Vsfold5: 0.506 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.26115971074e-07	? CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.652 Vsfold5: 0.522 Sensitivity CMfinder(20): 0.518 Vsfold5: 0.500 Positive Predictive Value CMfinder(20): 0.831 Vsfold5: 0.559 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.516 NanoFolder: 0.418 Sensitivity Vsfold5: 0.536 NanoFolder: 0.511 Positive Predictive Value Vsfold5: 0.509 NanoFolder: 0.356 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.723 RDfolder: 0.675 Sensitivity Vsfold5: 0.713 RDfolder: 0.636 Positive Predictive Value Vsfold5: 0.747 RDfolder: 0.733 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.557 RSpredict(seed): 0.314 Sensitivity Vsfold5: 0.565 RSpredict(seed): 0.177 Positive Predictive Value Vsfold5: 0.558 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.672 Vsfold5: 0.465 Sensitivity Multilign(seed): 0.615 Vsfold5: 0.453 Positive Predictive Value Multilign(seed): 0.748 Vsfold5: 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.513 PPfold(seed): 0.091 Sensitivity Vsfold5: 0.514 PPfold(seed): 0.016 Positive Predictive Value Vsfold5: 0.526 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.580 Carnac(seed): 0.282 Sensitivity Vsfold5: 0.576 Carnac(seed): 0.081 Positive Predictive Value Vsfold5: 0.595 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.556 Mastr(seed): 0.282 Sensitivity Vsfold5: 0.561 Mastr(seed): 0.090 Positive Predictive Value Vsfold5: 0.561 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Vsfold5: 0.177 Sensitivity PETfold_2.0(seed): 0.889 Vsfold5: 0.185 Positive Predictive Value PETfold_2.0(seed): 0.923 Vsfold5: 0.185 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Vsfold5: 0.177 Sensitivity PETfold_2.0(20): 0.889 Vsfold5: 0.185 Positive Predictive Value PETfold_2.0(20): 0.923 Vsfold5: 0.185 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RNAwolf	21 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.812 RNAwolf: 0.438 Sensitivity CentroidAlifold(20): 0.745 RNAwolf: 0.454 Positive Predictive Value CentroidAlifold(20): 0.890 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.866 RNAwolf: 0.494 Sensitivity PETfold_pre2.0(seed): 0.841 RNAwolf: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAwolf: 0.495 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	61 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.683 RNAwolf: 0.418 Sensitivity ContextFold: 0.677 RNAwolf: 0.428 Positive Predictive Value ContextFold: 0.691 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.774 RNAwolf: 0.502 Sensitivity MXScarna(seed): 0.740 RNAwolf: 0.502 Positive Predictive Value MXScarna(seed): 0.810 RNAwolf: 0.503 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.778 RNAwolf: 0.438 Sensitivity RNAalifold(20): 0.733 RNAwolf: 0.454 Positive Predictive Value RNAalifold(20): 0.831 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 RNAwolf: 0.392 Sensitivity PETfold_pre2.0(20): 0.776 RNAwolf: 0.410 Positive Predictive Value PETfold_pre2.0(20): 0.815 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	20 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.798 RNAwolf: 0.429 Sensitivity PPfold(20): 0.761 RNAwolf: 0.446 Positive Predictive Value PPfold(20): 0.840 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	69 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.669 RNAwolf: 0.436 Sensitivity IPknot: 0.645 RNAwolf: 0.446 Positive Predictive Value IPknot: 0.695 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.718 RNAwolf: 0.438 Sensitivity MXScarna(20): 0.699 RNAwolf: 0.454 Positive Predictive Value MXScarna(20): 0.743 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.716 RNAwolf: 0.438 Sensitivity RNASampler(20): 0.666 RNAwolf: 0.454 Positive Predictive Value RNASampler(20): 0.776 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.751 RNAwolf: 0.429 Sensitivity TurboFold(20): 0.741 RNAwolf: 0.446 Positive Predictive Value TurboFold(20): 0.766 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.764 RNAwolf: 0.509 Sensitivity CentroidAlifold(seed): 0.627 RNAwolf: 0.510 Positive Predictive Value CentroidAlifold(seed): 0.932 RNAwolf: 0.511 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	69 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.627 RNAwolf: 0.436 Sensitivity CentroidFold: 0.613 RNAwolf: 0.446 Positive Predictive Value CentroidFold: 0.644 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.611 RNAwolf: 0.436 Sensitivity Sfold: 0.614 RNAwolf: 0.446 Positive Predictive Value Sfold: 0.608 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.699 RNAwolf: 0.483 Sensitivity CentroidHomfold‑LAST: 0.637 RNAwolf: 0.494 Positive Predictive Value CentroidHomfold‑LAST: 0.773 RNAwolf: 0.483 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.609 RNAwolf: 0.436 Sensitivity Contrafold: 0.627 RNAwolf: 0.446 Positive Predictive Value Contrafold: 0.593 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.764 RNAwolf: 0.494 Sensitivity RNAalifold(seed): 0.667 RNAwolf: 0.497 Positive Predictive Value RNAalifold(seed): 0.876 RNAwolf: 0.493 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	69 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.588 RNAwolf: 0.436 Sensitivity MaxExpect: 0.606 RNAwolf: 0.446 Positive Predictive Value MaxExpect: 0.571 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.668 RNAwolf: 0.467 Sensitivity HotKnots: 0.699 RNAwolf: 0.481 Positive Predictive Value HotKnots: 0.644 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.582 RNAwolf: 0.436 Sensitivity UNAFold: 0.608 RNAwolf: 0.446 Positive Predictive Value UNAFold: 0.559 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.582 RNAwolf: 0.436 Sensitivity ProbKnot: 0.609 RNAwolf: 0.446 Positive Predictive Value ProbKnot: 0.559 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.705 RNAwolf: 0.438 Sensitivity Murlet(20): 0.637 RNAwolf: 0.454 Positive Predictive Value Murlet(20): 0.786 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	68 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.607 RNAwolf: 0.407 Sensitivity PknotsRG: 0.644 RNAwolf: 0.419 Positive Predictive Value PknotsRG: 0.574 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.587 RNAwolf: 0.436 Sensitivity RNAfold: 0.614 RNAwolf: 0.446 Positive Predictive Value RNAfold: 0.562 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.625 RNAwolf: 0.467 Sensitivity RNAshapes: 0.649 RNAwolf: 0.481 Positive Predictive Value RNAshapes: 0.609 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.549 RNAwolf: 0.436 Sensitivity Fold: 0.582 RNAwolf: 0.446 Positive Predictive Value Fold: 0.520 RNAwolf: 0.428 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.637 RNAwolf: 0.373 Sensitivity TurboFold(seed): 0.625 RNAwolf: 0.384 Positive Predictive Value TurboFold(seed): 0.658 RNAwolf: 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	38 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.525 RNAwolf: 0.393 Sensitivity Afold: 0.563 RNAwolf: 0.406 Positive Predictive Value Afold: 0.492 RNAwolf: 0.383 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.686 RNAwolf: 0.438 Sensitivity Carnac(20): 0.542 RNAwolf: 0.454 Positive Predictive Value Carnac(20): 0.873 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.627 RNAwolf: 0.429 Sensitivity RSpredict(20): 0.575 RNAwolf: 0.446 Positive Predictive Value RSpredict(20): 0.693 RNAwolf: 0.426 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	67 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.640 RNAwolf: 0.467 Sensitivity RNAsubopt: 0.677 RNAwolf: 0.481 Positive Predictive Value RNAsubopt: 0.612 RNAwolf: 0.464 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.625 RNAwolf: 0.505 Sensitivity Cylofold: 0.616 RNAwolf: 0.505 Positive Predictive Value Cylofold: 0.645 RNAwolf: 0.521 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.503 RNAwolf: 0.433 Sensitivity McQFold: 0.517 RNAwolf: 0.443 Positive Predictive Value McQFold: 0.491 RNAwolf: 0.425 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.582 RNAwolf: 0.441 Sensitivity RNASLOpt: 0.568 RNAwolf: 0.455 Positive Predictive Value RNASLOpt: 0.605 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	64 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.602 RNAwolf: 0.513 Sensitivity Pknots: 0.636 RNAwolf: 0.516 Positive Predictive Value Pknots: 0.581 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 64 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.683 RNAwolf: 0.552 Sensitivity CRWrnafold: 0.690 RNAwolf: 0.546 Positive Predictive Value CRWrnafold: 0.689 RNAwolf: 0.575 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.643 RNAwolf: 0.458 Sensitivity Multilign(20): 0.642 RNAwolf: 0.468 Positive Predictive Value Multilign(20): 0.652 RNAwolf: 0.462 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.76416234106e-08	9 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.497 RNAwolf: 0.424 Sensitivity RNASampler(seed): 0.412 RNAwolf: 0.464 Positive Predictive Value RNASampler(seed): 0.608 RNAwolf: 0.397 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	22 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.684 RNAwolf: 0.678 Sensitivity Alterna: 0.705 RNAwolf: 0.674 Positive Predictive Value Alterna: 0.679 RNAwolf: 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00114602237498	21 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.612 RNAwolf: 0.438 Sensitivity Mastr(20): 0.509 RNAwolf: 0.454 Positive Predictive Value Mastr(20): 0.744 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	60 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.550 RNAwolf: 0.524 Sensitivity Vsfold4: 0.542 RNAwolf: 0.530 Positive Predictive Value Vsfold4: 0.569 RNAwolf: 0.530 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.493 RNAwolf: 0.418 Sensitivity Murlet(seed): 0.320 RNAwolf: 0.431 Positive Predictive Value Murlet(seed): 0.769 RNAwolf: 0.420 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	58 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.550 RNAwolf: 0.495 Sensitivity MCFold: 0.586 RNAwolf: 0.501 Positive Predictive Value MCFold: 0.528 RNAwolf: 0.503 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold5: 0.505 Sensitivity RNAwolf: 0.524 Vsfold5: 0.518 Positive Predictive Value RNAwolf: 0.526 Vsfold5: 0.506 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.26115971074e-07		- CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.648 RNAwolf: 0.470 Sensitivity CMfinder(20): 0.563 RNAwolf: 0.489 Positive Predictive Value CMfinder(20): 0.754 RNAwolf: 0.462 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.505 NanoFolder: 0.395 Sensitivity RNAwolf: 0.515 NanoFolder: 0.495 Positive Predictive Value RNAwolf: 0.506 NanoFolder: 0.329 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.642 RDfolder: 0.578 Sensitivity RNAwolf: 0.634 RDfolder: 0.522 Positive Predictive Value RNAwolf: 0.667 RDfolder: 0.662 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.507 RSpredict(seed): 0.478 Sensitivity RNAwolf: 0.508 RSpredict(seed): 0.346 Positive Predictive Value RNAwolf: 0.508 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.6410608252e-08	- Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.658 RNAwolf: 0.452 Sensitivity Multilign(seed): 0.608 RNAwolf: 0.458 Positive Predictive Value Multilign(seed): 0.721 RNAwolf: 0.461 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.472 PPfold(seed): 0.157 Sensitivity RNAwolf: 0.479 PPfold(seed): 0.040 Positive Predictive Value RNAwolf: 0.478 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.543 RNAwolf: 0.487 Sensitivity Carnac(seed): 0.317 RNAwolf: 0.488 Positive Predictive Value Carnac(seed): 0.934 RNAwolf: 0.488 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.47424713927e-05	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.477 Mastr(seed): 0.040 Sensitivity RNAwolf: 0.484 Mastr(seed): 0.004 Positive Predictive Value RNAwolf: 0.482 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNAwolf: 0.704 Sensitivity PETfold_2.0(seed): 0.845 RNAwolf: 0.690 Positive Predictive Value PETfold_2.0(seed): 0.891 RNAwolf: 0.727 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAwolf: 0.588 Sensitivity PETfold_2.0(20): 0.889 RNAwolf: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 RNAwolf: 0.593 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CMfinder(20)	11 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 CMfinder(20): 0.648 Sensitivity CentroidAlifold(20): 0.783 CMfinder(20): 0.563 Positive Predictive Value CentroidAlifold(20): 0.866 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	11 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.917 CMfinder(20): 0.648 Sensitivity PETfold_pre2.0(seed): 0.908 CMfinder(20): 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.929 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	4 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.908 CMfinder(20): 0.652 Sensitivity ContextFold: 0.860 CMfinder(20): 0.518 Positive Predictive Value ContextFold: 0.961 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.776 CMfinder(20): 0.652 Sensitivity MXScarna(seed): 0.737 CMfinder(20): 0.518 Positive Predictive Value MXScarna(seed): 0.824 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.888 CMfinder(20): 0.652 Sensitivity RNAalifold(20): 0.816 CMfinder(20): 0.518 Positive Predictive Value RNAalifold(20): 0.969 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 CMfinder(20): 0.648 Sensitivity PETfold_pre2.0(20): 0.846 CMfinder(20): 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.855 CMfinder(20): 0.754 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	4 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.927 CMfinder(20): 0.652 Sensitivity PPfold(20): 0.895 CMfinder(20): 0.518 Positive Predictive Value PPfold(20): 0.962 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.749 CMfinder(20): 0.652 Sensitivity IPknot: 0.746 CMfinder(20): 0.518 Positive Predictive Value IPknot: 0.759 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.772 CMfinder(20): 0.652 Sensitivity MXScarna(20): 0.737 CMfinder(20): 0.518 Positive Predictive Value MXScarna(20): 0.816 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.721 CMfinder(20): 0.652 Sensitivity RNASampler(20): 0.640 CMfinder(20): 0.518 Positive Predictive Value RNASampler(20): 0.820 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.872 CMfinder(20): 0.652 Sensitivity TurboFold(20): 0.842 CMfinder(20): 0.518 Positive Predictive Value TurboFold(20): 0.906 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.648 CentroidAlifold(seed): 0.630 Sensitivity CMfinder(20): 0.563 CentroidAlifold(seed): 0.430 Positive Predictive Value CMfinder(20): 0.754 CentroidAlifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.48061257066e-07	11 CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.648 CentroidFold: 0.645 Sensitivity CMfinder(20): 0.563 CentroidFold: 0.680 Positive Predictive Value CMfinder(20): 0.754 CentroidFold: 0.619 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00868291460752	4 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.729 CMfinder(20): 0.652 Sensitivity Sfold: 0.719 CMfinder(20): 0.518 Positive Predictive Value Sfold: 0.745 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.691 CMfinder(20): 0.652 Sensitivity CentroidHomfold‑LAST: 0.737 CMfinder(20): 0.518 Positive Predictive Value CentroidHomfold‑LAST: 0.656 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.735 CMfinder(20): 0.652 Sensitivity Contrafold: 0.746 CMfinder(20): 0.518 Positive Predictive Value Contrafold: 0.733 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	1 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.839 CMfinder(20): 0.536 Sensitivity RNAalifold(seed): 0.708 CMfinder(20): 0.292 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.653 CMfinder(20): 0.652 Sensitivity MaxExpect: 0.640 CMfinder(20): 0.518 Positive Predictive Value MaxExpect: 0.676 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: 0.686 CMfinder(20): 0.652 Sensitivity HotKnots: 0.693 CMfinder(20): 0.518 Positive Predictive Value HotKnots: 0.687 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.674 CMfinder(20): 0.652 Sensitivity UNAFold: 0.684 CMfinder(20): 0.518 Positive Predictive Value UNAFold: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.687 CMfinder(20): 0.652 Sensitivity ProbKnot: 0.675 CMfinder(20): 0.518 Positive Predictive Value ProbKnot: 0.706 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.696 CMfinder(20): 0.652 Sensitivity Murlet(20): 0.632 CMfinder(20): 0.518 Positive Predictive Value Murlet(20): 0.774 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.674 CMfinder(20): 0.652 Sensitivity PknotsRG: 0.684 CMfinder(20): 0.518 Positive Predictive Value PknotsRG: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.674 CMfinder(20): 0.652 Sensitivity RNAfold: 0.684 CMfinder(20): 0.518 Positive Predictive Value RNAfold: 0.672 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: 0.659 CMfinder(20): 0.652 Sensitivity RNAshapes: 0.667 CMfinder(20): 0.518 Positive Predictive Value RNAshapes: 0.661 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.653 CMfinder(20): 0.652 Sensitivity Fold: 0.667 CMfinder(20): 0.518 Positive Predictive Value Fold: 0.650 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.818 CMfinder(20): 0.698 Sensitivity Afold: 0.771 CMfinder(20): 0.543 Positive Predictive Value Afold: 0.871 CMfinder(20): 0.905 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.654 CMfinder(20): 0.652 Sensitivity Carnac(20): 0.544 CMfinder(20): 0.518 Positive Predictive Value Carnac(20): 0.795 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	10 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.688 CMfinder(20): 0.660 Sensitivity RSpredict(20): 0.653 CMfinder(20): 0.580 Positive Predictive Value RSpredict(20): 0.731 CMfinder(20): 0.759 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.62909925123e-09	4 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.685 CMfinder(20): 0.652 Sensitivity RNAsubopt: 0.702 CMfinder(20): 0.518 Positive Predictive Value RNAsubopt: 0.678 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.754 CMfinder(20): 0.652 Sensitivity Cylofold: 0.737 CMfinder(20): 0.518 Positive Predictive Value Cylofold: 0.778 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: 0.774 CMfinder(20): 0.652 Sensitivity McQFold: 0.728 CMfinder(20): 0.518 Positive Predictive Value McQFold: 0.830 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.733 CMfinder(20): 0.652 Sensitivity RNASLOpt: 0.693 CMfinder(20): 0.518 Positive Predictive Value RNASLOpt: 0.782 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.652 Pknots: 0.618 Sensitivity CMfinder(20): 0.518 Pknots: 0.623 Positive Predictive Value CMfinder(20): 0.831 Pknots: 0.623 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.672 CMfinder(20): 0.652 Sensitivity Multilign(20): 0.649 CMfinder(20): 0.518 Positive Predictive Value Multilign(20): 0.705 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): 0.669 CMfinder(20): 0.652 Sensitivity Mastr(20): 0.570 CMfinder(20): 0.518 Positive Predictive Value Mastr(20): 0.793 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.721 CMfinder(20): 0.652 Sensitivity Vsfold4: 0.702 CMfinder(20): 0.518 Positive Predictive Value Vsfold4: 0.748 CMfinder(20): 0.831 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	1 CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.536 Murlet(seed): 0.165 Sensitivity CMfinder(20): 0.292 Murlet(seed): 0.125 Positive Predictive Value CMfinder(20): 1.000 Murlet(seed): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	10 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.660 MCFold: 0.477 Sensitivity CMfinder(20): 0.580 MCFold: 0.543 Positive Predictive Value CMfinder(20): 0.759 MCFold: 0.429 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	4 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.652 Vsfold5: 0.522 Sensitivity CMfinder(20): 0.518 Vsfold5: 0.500 Positive Predictive Value CMfinder(20): 0.831 Vsfold5: 0.559 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.648 RNAwolf: 0.470 Sensitivity CMfinder(20): 0.563 RNAwolf: 0.489 Positive Predictive Value CMfinder(20): 0.754 RNAwolf: 0.462 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08		? CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.629 NanoFolder: 0.218 Sensitivity CMfinder(20): 0.522 NanoFolder: 0.275 Positive Predictive Value CMfinder(20): 0.766 NanoFolder: 0.190 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.844 RDfolder: 0.820 Sensitivity CMfinder(20): 0.762 RDfolder: 0.762 Positive Predictive Value CMfinder(20): 0.941 RDfolder: 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.660 RSpredict(seed): 0.017 Sensitivity CMfinder(20): 0.580 RSpredict(seed): 0.008 Positive Predictive Value CMfinder(20): 0.759 RSpredict(seed): 0.054 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	? Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.652 PPfold(seed): 0.000 Sensitivity CMfinder(20): 0.518 PPfold(seed): 0.000 Positive Predictive Value CMfinder(20): 0.831 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.536 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.292 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.652 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.831 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CMfinder(20): 0.526 Sensitivity PETfold_2.0(seed): 0.889 CMfinder(20): 0.407 Positive Predictive Value PETfold_2.0(seed): 0.923 CMfinder(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CMfinder(20): 0.526 Sensitivity PETfold_2.0(20): 0.889 CMfinder(20): 0.407 Positive Predictive Value PETfold_2.0(20): 0.923 CMfinder(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
NanoFolder	14 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.813 NanoFolder: 0.322 Sensitivity CentroidAlifold(20): 0.761 NanoFolder: 0.414 Positive Predictive Value CentroidAlifold(20): 0.872 NanoFolder: 0.264 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.62913390836e-08	19 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.883 NanoFolder: 0.340 Sensitivity PETfold_pre2.0(seed): 0.848 NanoFolder: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.922 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	25 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.738 NanoFolder: 0.394 Sensitivity ContextFold: 0.717 NanoFolder: 0.485 Positive Predictive Value ContextFold: 0.765 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.753 NanoFolder: 0.338 Sensitivity MXScarna(seed): 0.712 NanoFolder: 0.414 Positive Predictive Value MXScarna(seed): 0.802 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	7 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.788 NanoFolder: 0.329 Sensitivity RNAalifold(20): 0.732 NanoFolder: 0.405 Positive Predictive Value RNAalifold(20): 0.853 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	14 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.823 NanoFolder: 0.322 Sensitivity PETfold_pre2.0(20): 0.816 NanoFolder: 0.414 Positive Predictive Value PETfold_pre2.0(20): 0.833 NanoFolder: 0.264 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.06323189071e-08	7 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.848 NanoFolder: 0.329 Sensitivity PPfold(20): 0.816 NanoFolder: 0.405 Positive Predictive Value PPfold(20): 0.886 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.750 NanoFolder: 0.394 Sensitivity IPknot: 0.749 NanoFolder: 0.485 Positive Predictive Value IPknot: 0.758 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.709 NanoFolder: 0.329 Sensitivity MXScarna(20): 0.689 NanoFolder: 0.405 Positive Predictive Value MXScarna(20): 0.736 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.724 NanoFolder: 0.329 Sensitivity RNASampler(20): 0.653 NanoFolder: 0.405 Positive Predictive Value RNASampler(20): 0.810 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.773 NanoFolder: 0.329 Sensitivity TurboFold(20): 0.742 NanoFolder: 0.405 Positive Predictive Value TurboFold(20): 0.810 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	19 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.643 NanoFolder: 0.340 Sensitivity CentroidAlifold(seed): 0.441 NanoFolder: 0.430 Positive Predictive Value CentroidAlifold(seed): 0.944 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	36 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.667 NanoFolder: 0.395 Sensitivity CentroidFold: 0.673 NanoFolder: 0.495 Positive Predictive Value CentroidFold: 0.668 NanoFolder: 0.329 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.681 NanoFolder: 0.394 Sensitivity Sfold: 0.679 NanoFolder: 0.485 Positive Predictive Value Sfold: 0.692 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.752 NanoFolder: 0.374 Sensitivity CentroidHomfold‑LAST: 0.698 NanoFolder: 0.463 Positive Predictive Value CentroidHomfold‑LAST: 0.816 NanoFolder: 0.317 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.687 NanoFolder: 0.394 Sensitivity Contrafold: 0.703 NanoFolder: 0.485 Positive Predictive Value Contrafold: 0.679 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.581 NanoFolder: 0.294 Sensitivity RNAalifold(seed): 0.426 NanoFolder: 0.357 Positive Predictive Value RNAalifold(seed): 0.803 NanoFolder: 0.259 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	25 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.690 NanoFolder: 0.394 Sensitivity MaxExpect: 0.701 NanoFolder: 0.485 Positive Predictive Value MaxExpect: 0.687 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.692 NanoFolder: 0.394 Sensitivity HotKnots: 0.717 NanoFolder: 0.485 Positive Predictive Value HotKnots: 0.675 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.658 NanoFolder: 0.394 Sensitivity UNAFold: 0.673 NanoFolder: 0.485 Positive Predictive Value UNAFold: 0.651 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.694 NanoFolder: 0.394 Sensitivity ProbKnot: 0.723 NanoFolder: 0.485 Positive Predictive Value ProbKnot: 0.673 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	7 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.714 NanoFolder: 0.329 Sensitivity Murlet(20): 0.637 NanoFolder: 0.405 Positive Predictive Value Murlet(20): 0.807 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.701 NanoFolder: 0.394 Sensitivity PknotsRG: 0.725 NanoFolder: 0.485 Positive Predictive Value PknotsRG: 0.685 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.703 NanoFolder: 0.394 Sensitivity RNAfold: 0.717 NanoFolder: 0.485 Positive Predictive Value RNAfold: 0.696 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.663 NanoFolder: 0.394 Sensitivity RNAshapes: 0.683 NanoFolder: 0.485 Positive Predictive Value RNAshapes: 0.651 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.720 NanoFolder: 0.394 Sensitivity Fold: 0.739 NanoFolder: 0.485 Positive Predictive Value Fold: 0.709 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.532 NanoFolder: 0.410 Sensitivity TurboFold(seed): 0.521 NanoFolder: 0.496 Positive Predictive Value TurboFold(seed): 0.554 NanoFolder: 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	17 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.632 NanoFolder: 0.445 Sensitivity Afold: 0.667 NanoFolder: 0.549 Positive Predictive Value Afold: 0.608 NanoFolder: 0.374 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	7 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.671 NanoFolder: 0.329 Sensitivity Carnac(20): 0.542 NanoFolder: 0.405 Positive Predictive Value Carnac(20): 0.837 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.618 NanoFolder: 0.326 Sensitivity RSpredict(20): 0.573 NanoFolder: 0.417 Positive Predictive Value RSpredict(20): 0.674 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	25 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.656 NanoFolder: 0.394 Sensitivity RNAsubopt: 0.683 NanoFolder: 0.485 Positive Predictive Value RNAsubopt: 0.638 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.621 NanoFolder: 0.438 Sensitivity Cylofold: 0.620 NanoFolder: 0.529 Positive Predictive Value Cylofold: 0.633 NanoFolder: 0.378 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.582 NanoFolder: 0.380 Sensitivity McQFold: 0.593 NanoFolder: 0.470 Positive Predictive Value McQFold: 0.582 NanoFolder: 0.321 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.627 NanoFolder: 0.394 Sensitivity RNASLOpt: 0.592 NanoFolder: 0.485 Positive Predictive Value RNASLOpt: 0.673 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	24 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.601 NanoFolder: 0.429 Sensitivity Pknots: 0.624 NanoFolder: 0.516 Positive Predictive Value Pknots: 0.589 NanoFolder: 0.373 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	14 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.687 NanoFolder: 0.542 Sensitivity CRWrnafold: 0.694 NanoFolder: 0.635 Positive Predictive Value CRWrnafold: 0.689 NanoFolder: 0.478 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	7 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.731 NanoFolder: 0.329 Sensitivity Multilign(20): 0.726 NanoFolder: 0.405 Positive Predictive Value Multilign(20): 0.742 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.361 NanoFolder: 0.195 Sensitivity RNASampler(seed): 0.282 NanoFolder: 0.254 Positive Predictive Value RNASampler(seed): 0.476 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.756 NanoFolder: 0.610 Sensitivity Alterna: 0.753 NanoFolder: 0.706 Positive Predictive Value Alterna: 0.771 NanoFolder: 0.545 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.595 NanoFolder: 0.329 Sensitivity Mastr(20): 0.511 NanoFolder: 0.405 Positive Predictive Value Mastr(20): 0.703 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.571 NanoFolder: 0.394 Sensitivity Vsfold4: 0.570 NanoFolder: 0.485 Positive Predictive Value Vsfold4: 0.583 NanoFolder: 0.334 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.466 NanoFolder: 0.294 Sensitivity Murlet(seed): 0.313 NanoFolder: 0.357 Positive Predictive Value Murlet(seed): 0.706 NanoFolder: 0.259 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.574 NanoFolder: 0.440 Sensitivity MCFold: 0.606 NanoFolder: 0.545 Positive Predictive Value MCFold: 0.554 NanoFolder: 0.369 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.516 NanoFolder: 0.418 Sensitivity Vsfold5: 0.536 NanoFolder: 0.511 Positive Predictive Value Vsfold5: 0.509 NanoFolder: 0.356 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.505 NanoFolder: 0.395 Sensitivity RNAwolf: 0.515 NanoFolder: 0.495 Positive Predictive Value RNAwolf: 0.506 NanoFolder: 0.329 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.629 NanoFolder: 0.218 Sensitivity CMfinder(20): 0.522 NanoFolder: 0.275 Positive Predictive Value CMfinder(20): 0.766 NanoFolder: 0.190 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		+ NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.548 RDfolder: 0.507 Sensitivity NanoFolder: 0.613 RDfolder: 0.470 Positive Predictive Value NanoFolder: 0.512 RDfolder: 0.572 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.90637340822e-08	+ NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.344 RSpredict(seed): 0.106 Sensitivity NanoFolder: 0.434 RSpredict(seed): 0.053 Positive Predictive Value NanoFolder: 0.287 RSpredict(seed): 0.230 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.660 NanoFolder: 0.333 Sensitivity Multilign(seed): 0.600 NanoFolder: 0.375 Positive Predictive Value Multilign(seed): 0.738 NanoFolder: 0.323 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.338 PPfold(seed): 0.114 Sensitivity NanoFolder: 0.414 PPfold(seed): 0.025 Positive Predictive Value NanoFolder: 0.293 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.363 Carnac(seed): 0.161 Sensitivity NanoFolder: 0.434 Carnac(seed): 0.026 Positive Predictive Value NanoFolder: 0.319 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.338 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.414 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.293 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.82838438772e-09	? NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 NanoFolder: 0.281 Sensitivity PETfold_2.0(seed): 0.889 NanoFolder: 0.370 Positive Predictive Value PETfold_2.0(seed): 0.923 NanoFolder: 0.227 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.905 NanoFolder: 0.281 Sensitivity PETfold_2.0(20): 0.889 NanoFolder: 0.370 Positive Predictive Value PETfold_2.0(20): 0.923 NanoFolder: 0.227 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RDfolder	17 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.878 RDfolder: 0.633 Sensitivity CentroidAlifold(20): 0.810 RDfolder: 0.601 Positive Predictive Value CentroidAlifold(20): 0.956 RDfolder: 0.681 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	8 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.801 RDfolder: 0.432 Sensitivity PETfold_pre2.0(seed): 0.749 RDfolder: 0.398 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.493 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	21 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.776 RDfolder: 0.546 Sensitivity ContextFold: 0.734 RDfolder: 0.494 Positive Predictive Value ContextFold: 0.832 RDfolder: 0.625 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	33 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.808 RDfolder: 0.626 Sensitivity MXScarna(seed): 0.754 RDfolder: 0.592 Positive Predictive Value MXScarna(seed): 0.874 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.847 RDfolder: 0.636 Sensitivity RNAalifold(20): 0.764 RDfolder: 0.602 Positive Predictive Value RNAalifold(20): 0.945 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	5 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.826 RDfolder: 0.595 Sensitivity PETfold_pre2.0(20): 0.778 RDfolder: 0.545 Positive Predictive Value PETfold_pre2.0(20): 0.885 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.829 RDfolder: 0.584 Sensitivity PPfold(20): 0.753 RDfolder: 0.518 Positive Predictive Value PPfold(20): 0.921 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	29 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.756 RDfolder: 0.568 Sensitivity IPknot: 0.728 RDfolder: 0.514 Positive Predictive Value IPknot: 0.797 RDfolder: 0.648 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.812 RDfolder: 0.636 Sensitivity MXScarna(20): 0.755 RDfolder: 0.602 Positive Predictive Value MXScarna(20): 0.880 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	17 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.883 RDfolder: 0.636 Sensitivity RNASampler(20): 0.805 RDfolder: 0.602 Positive Predictive Value RNASampler(20): 0.972 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.74172190343e-08	8 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.776 RDfolder: 0.584 Sensitivity TurboFold(20): 0.724 RDfolder: 0.518 Positive Predictive Value TurboFold(20): 0.842 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	33 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.688 RDfolder: 0.624 Sensitivity CentroidAlifold(seed): 0.543 RDfolder: 0.592 Positive Predictive Value CentroidAlifold(seed): 0.883 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.48494289621e-08	86 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.830 RDfolder: 0.659 Sensitivity CentroidFold: 0.810 RDfolder: 0.618 Positive Predictive Value CentroidFold: 0.858 RDfolder: 0.719 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.812 RDfolder: 0.677 Sensitivity Sfold: 0.793 RDfolder: 0.637 Positive Predictive Value Sfold: 0.841 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.798 RDfolder: 0.611 Sensitivity CentroidHomfold‑LAST: 0.727 RDfolder: 0.560 Positive Predictive Value CentroidHomfold‑LAST: 0.887 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.835 RDfolder: 0.677 Sensitivity Contrafold: 0.829 RDfolder: 0.637 Positive Predictive Value Contrafold: 0.849 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.740 RDfolder: 0.644 Sensitivity RNAalifold(seed): 0.624 RDfolder: 0.592 Positive Predictive Value RNAalifold(seed): 0.889 RDfolder: 0.717 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	77 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.801 RDfolder: 0.668 Sensitivity MaxExpect: 0.799 RDfolder: 0.625 Positive Predictive Value MaxExpect: 0.812 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.823 RDfolder: 0.677 Sensitivity HotKnots: 0.830 RDfolder: 0.637 Positive Predictive Value HotKnots: 0.824 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.815 RDfolder: 0.677 Sensitivity UNAFold: 0.812 RDfolder: 0.637 Positive Predictive Value UNAFold: 0.827 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.801 RDfolder: 0.675 Sensitivity ProbKnot: 0.823 RDfolder: 0.639 Positive Predictive Value ProbKnot: 0.791 RDfolder: 0.729 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.759 RDfolder: 0.636 Sensitivity Murlet(20): 0.661 RDfolder: 0.602 Positive Predictive Value Murlet(20): 0.882 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	96 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.800 RDfolder: 0.677 Sensitivity PknotsRG: 0.806 RDfolder: 0.637 Positive Predictive Value PknotsRG: 0.804 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.802 RDfolder: 0.677 Sensitivity RNAfold: 0.803 RDfolder: 0.637 Positive Predictive Value RNAfold: 0.810 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.793 RDfolder: 0.677 Sensitivity RNAshapes: 0.787 RDfolder: 0.637 Positive Predictive Value RNAshapes: 0.810 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.816 RDfolder: 0.686 Sensitivity Fold: 0.820 RDfolder: 0.647 Positive Predictive Value Fold: 0.821 RDfolder: 0.744 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.680 RDfolder: 0.528 Sensitivity TurboFold(seed): 0.622 RDfolder: 0.459 Positive Predictive Value TurboFold(seed): 0.760 RDfolder: 0.630 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	74 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.801 RDfolder: 0.704 Sensitivity Afold: 0.811 RDfolder: 0.663 Positive Predictive Value Afold: 0.803 RDfolder: 0.762 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.726 RDfolder: 0.636 Sensitivity Carnac(20): 0.581 RDfolder: 0.602 Positive Predictive Value Carnac(20): 0.916 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	18 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.752 RDfolder: 0.644 Sensitivity RSpredict(20): 0.668 RDfolder: 0.612 Positive Predictive Value RSpredict(20): 0.857 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	96 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.790 RDfolder: 0.677 Sensitivity RNAsubopt: 0.790 RDfolder: 0.637 Positive Predictive Value RNAsubopt: 0.801 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.783 RDfolder: 0.654 Sensitivity Cylofold: 0.763 RDfolder: 0.618 Positive Predictive Value Cylofold: 0.815 RDfolder: 0.709 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.798 RDfolder: 0.677 Sensitivity McQFold: 0.767 RDfolder: 0.637 Positive Predictive Value McQFold: 0.840 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.683 RDfolder: 0.546 Sensitivity RNASLOpt: 0.639 RDfolder: 0.494 Positive Predictive Value RNASLOpt: 0.747 RDfolder: 0.625 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	96 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.802 RDfolder: 0.677 Sensitivity Pknots: 0.809 RDfolder: 0.637 Positive Predictive Value Pknots: 0.804 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.703 RDfolder: 0.530 Sensitivity CRWrnafold: 0.704 RDfolder: 0.479 Positive Predictive Value CRWrnafold: 0.717 RDfolder: 0.610 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.716 RDfolder: 0.584 Sensitivity Multilign(20): 0.694 RDfolder: 0.518 Positive Predictive Value Multilign(20): 0.752 RDfolder: 0.677 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	15 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.798 RDfolder: 0.686 Sensitivity RNASampler(seed): 0.679 RDfolder: 0.617 Positive Predictive Value RNASampler(seed): 0.948 RDfolder: 0.778 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.29277699493e-09	88 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.768 RDfolder: 0.690 Sensitivity Alterna: 0.777 RDfolder: 0.652 Positive Predictive Value Alterna: 0.771 RDfolder: 0.745 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.777 RDfolder: 0.636 Sensitivity Mastr(20): 0.693 RDfolder: 0.602 Positive Predictive Value Mastr(20): 0.880 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	96 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.751 RDfolder: 0.677 Sensitivity Vsfold4: 0.724 RDfolder: 0.637 Positive Predictive Value Vsfold4: 0.791 RDfolder: 0.735 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.642 RDfolder: 0.633 Sensitivity Murlet(seed): 0.494 RDfolder: 0.582 Positive Predictive Value Murlet(seed): 0.850 RDfolder: 0.707 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.00102881663438	95 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.705 MCFold: 0.698 Sensitivity RDfolder: 0.659 MCFold: 0.733 Positive Predictive Value RDfolder: 0.769 MCFold: 0.680 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 0.0133909664952	95 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.723 RDfolder: 0.675 Sensitivity Vsfold5: 0.713 RDfolder: 0.636 Positive Predictive Value Vsfold5: 0.747 RDfolder: 0.733 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.642 RDfolder: 0.578 Sensitivity RNAwolf: 0.634 RDfolder: 0.522 Positive Predictive Value RNAwolf: 0.667 RDfolder: 0.662 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	1 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.844 RDfolder: 0.820 Sensitivity CMfinder(20): 0.762 RDfolder: 0.762 Positive Predictive Value CMfinder(20): 0.941 RDfolder: 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	11 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.548 RDfolder: 0.507 Sensitivity NanoFolder: 0.613 RDfolder: 0.470 Positive Predictive Value NanoFolder: 0.512 RDfolder: 0.572 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.90637340822e-08		+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.630 RSpredict(seed): 0.478 Sensitivity RDfolder: 0.598 RSpredict(seed): 0.326 Positive Predictive Value RDfolder: 0.679 RSpredict(seed): 0.721 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.737 RDfolder: 0.483 Sensitivity Multilign(seed): 0.689 RDfolder: 0.430 Positive Predictive Value Multilign(seed): 0.800 RDfolder: 0.565 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.422 PPfold(seed): 0.139 Sensitivity RDfolder: 0.375 PPfold(seed): 0.027 Positive Predictive Value RDfolder: 0.497 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.633 Carnac(seed): 0.374 Sensitivity RDfolder: 0.582 Carnac(seed): 0.143 Positive Predictive Value RDfolder: 0.707 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.626 Mastr(seed): 0.390 Sensitivity RDfolder: 0.592 Mastr(seed): 0.173 Positive Predictive Value RDfolder: 0.677 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RSpredict(seed)	38 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.807 RSpredict(seed): 0.219 Sensitivity CentroidAlifold(20): 0.726 RSpredict(seed): 0.107 Positive Predictive Value CentroidAlifold(20): 0.901 RSpredict(seed): 0.461 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.853 RSpredict(seed): 0.515 Sensitivity PETfold_pre2.0(seed): 0.822 RSpredict(seed): 0.388 Positive Predictive Value PETfold_pre2.0(seed): 0.885 RSpredict(seed): 0.686 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.800 RSpredict(seed): 0.480 Sensitivity ContextFold: 0.779 RSpredict(seed): 0.353 Positive Predictive Value ContextFold: 0.823 RSpredict(seed): 0.655 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	60 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.780 RSpredict(seed): 0.453 Sensitivity MXScarna(seed): 0.745 RSpredict(seed): 0.307 Positive Predictive Value MXScarna(seed): 0.819 RSpredict(seed): 0.670 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.779 RSpredict(seed): 0.230 Sensitivity RNAalifold(20): 0.704 RSpredict(seed): 0.114 Positive Predictive Value RNAalifold(20): 0.866 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 RSpredict(seed): 0.365 Sensitivity PETfold_pre2.0(20): 0.763 RSpredict(seed): 0.220 Positive Predictive Value PETfold_pre2.0(20): 0.823 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	21 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.793 RSpredict(seed): 0.180 Sensitivity PPfold(20): 0.752 RSpredict(seed): 0.086 Positive Predictive Value PPfold(20): 0.841 RSpredict(seed): 0.394 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.81788725234e-08	28 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.721 RSpredict(seed): 0.478 Sensitivity IPknot: 0.708 RSpredict(seed): 0.346 Positive Predictive Value IPknot: 0.736 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.745 RSpredict(seed): 0.230 Sensitivity MXScarna(20): 0.719 RSpredict(seed): 0.114 Positive Predictive Value MXScarna(20): 0.776 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.737 RSpredict(seed): 0.230 Sensitivity RNASampler(20): 0.667 RSpredict(seed): 0.114 Positive Predictive Value RNASampler(20): 0.820 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.758 RSpredict(seed): 0.180 Sensitivity TurboFold(20): 0.748 RSpredict(seed): 0.086 Positive Predictive Value TurboFold(20): 0.773 RSpredict(seed): 0.394 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	60 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.735 RSpredict(seed): 0.446 Sensitivity CentroidAlifold(seed): 0.604 RSpredict(seed): 0.302 Positive Predictive Value CentroidAlifold(seed): 0.895 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.718 RSpredict(seed): 0.446 Sensitivity CentroidFold: 0.718 RSpredict(seed): 0.302 Positive Predictive Value CentroidFold: 0.720 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.670 RSpredict(seed): 0.449 Sensitivity Sfold: 0.667 RSpredict(seed): 0.304 Positive Predictive Value Sfold: 0.675 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 RSpredict(seed): 0.171 Sensitivity CentroidHomfold‑LAST: 0.710 RSpredict(seed): 0.087 Positive Predictive Value CentroidHomfold‑LAST: 0.725 RSpredict(seed): 0.356 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	61 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.700 RSpredict(seed): 0.449 Sensitivity Contrafold: 0.724 RSpredict(seed): 0.304 Positive Predictive Value Contrafold: 0.679 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.733 RSpredict(seed): 0.553 Sensitivity RNAalifold(seed): 0.610 RSpredict(seed): 0.419 Positive Predictive Value RNAalifold(seed): 0.883 RSpredict(seed): 0.733 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.671 RSpredict(seed): 0.448 Sensitivity MaxExpect: 0.688 RSpredict(seed): 0.305 Positive Predictive Value MaxExpect: 0.657 RSpredict(seed): 0.661 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.672 RSpredict(seed): 0.316 Sensitivity HotKnots: 0.707 RSpredict(seed): 0.179 Positive Predictive Value HotKnots: 0.645 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.649 RSpredict(seed): 0.449 Sensitivity UNAFold: 0.670 RSpredict(seed): 0.304 Positive Predictive Value UNAFold: 0.631 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.646 RSpredict(seed): 0.425 Sensitivity ProbKnot: 0.671 RSpredict(seed): 0.286 Positive Predictive Value ProbKnot: 0.623 RSpredict(seed): 0.634 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.697 RSpredict(seed): 0.230 Sensitivity Murlet(20): 0.604 RSpredict(seed): 0.114 Positive Predictive Value Murlet(20): 0.810 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.691 RSpredict(seed): 0.316 Sensitivity PknotsRG: 0.723 RSpredict(seed): 0.179 Positive Predictive Value PknotsRG: 0.666 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.659 RSpredict(seed): 0.449 Sensitivity RNAfold: 0.683 RSpredict(seed): 0.304 Positive Predictive Value RNAfold: 0.638 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.680 RSpredict(seed): 0.316 Sensitivity RNAshapes: 0.703 RSpredict(seed): 0.179 Positive Predictive Value RNAshapes: 0.663 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.658 RSpredict(seed): 0.444 Sensitivity Fold: 0.687 RSpredict(seed): 0.304 Positive Predictive Value Fold: 0.632 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.653 RSpredict(seed): 0.278 Sensitivity TurboFold(seed): 0.641 RSpredict(seed): 0.154 Positive Predictive Value TurboFold(seed): 0.674 RSpredict(seed): 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.11142658008e-08	35 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.650 RSpredict(seed): 0.426 Sensitivity Afold: 0.684 RSpredict(seed): 0.268 Positive Predictive Value Afold: 0.624 RSpredict(seed): 0.685 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	39 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.693 RSpredict(seed): 0.230 Sensitivity Carnac(20): 0.526 RSpredict(seed): 0.114 Positive Predictive Value Carnac(20): 0.917 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.664 RSpredict(seed): 0.341 Sensitivity RSpredict(20): 0.601 RSpredict(seed): 0.194 Positive Predictive Value RSpredict(20): 0.736 RSpredict(seed): 0.604 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.667 RSpredict(seed): 0.316 Sensitivity RNAsubopt: 0.701 RSpredict(seed): 0.179 Positive Predictive Value RNAsubopt: 0.642 RSpredict(seed): 0.572 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.704 RSpredict(seed): 0.266 Sensitivity Cylofold: 0.694 RSpredict(seed): 0.148 Positive Predictive Value Cylofold: 0.723 RSpredict(seed): 0.498 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	61 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.624 RSpredict(seed): 0.449 Sensitivity McQFold: 0.636 RSpredict(seed): 0.304 Positive Predictive Value McQFold: 0.616 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.591 RSpredict(seed): 0.135 Sensitivity RNASLOpt: 0.578 RSpredict(seed): 0.067 Positive Predictive Value RNASLOpt: 0.613 RSpredict(seed): 0.291 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	58 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.668 RSpredict(seed): 0.326 Sensitivity Pknots: 0.704 RSpredict(seed): 0.187 Positive Predictive Value Pknots: 0.643 RSpredict(seed): 0.584 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 RSpredict(seed): 0.126 Sensitivity CRWrnafold: 0.655 RSpredict(seed): 0.059 Positive Predictive Value CRWrnafold: 0.649 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	21 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.625 RSpredict(seed): 0.198 Sensitivity Multilign(20): 0.611 RSpredict(seed): 0.095 Positive Predictive Value Multilign(20): 0.649 RSpredict(seed): 0.432 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	22 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.689 RSpredict(seed): 0.546 Sensitivity RNASampler(seed): 0.602 RSpredict(seed): 0.406 Positive Predictive Value RNASampler(seed): 0.795 RSpredict(seed): 0.744 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	29 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.757 RSpredict(seed): 0.502 Sensitivity Alterna: 0.765 RSpredict(seed): 0.350 Positive Predictive Value Alterna: 0.760 RSpredict(seed): 0.739 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	39 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.626 RSpredict(seed): 0.230 Sensitivity Mastr(20): 0.487 RSpredict(seed): 0.114 Positive Predictive Value Mastr(20): 0.812 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.592 RSpredict(seed): 0.318 Sensitivity Vsfold4: 0.592 RSpredict(seed): 0.181 Positive Predictive Value Vsfold4: 0.599 RSpredict(seed): 0.573 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.583 RSpredict(seed): 0.467 Sensitivity Murlet(seed): 0.401 RSpredict(seed): 0.310 Positive Predictive Value Murlet(seed): 0.857 RSpredict(seed): 0.715 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.557 RSpredict(seed): 0.331 Sensitivity MCFold: 0.608 RSpredict(seed): 0.191 Positive Predictive Value MCFold: 0.521 RSpredict(seed): 0.591 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.557 RSpredict(seed): 0.314 Sensitivity Vsfold5: 0.565 RSpredict(seed): 0.177 Positive Predictive Value Vsfold5: 0.558 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.507 RSpredict(seed): 0.478 Sensitivity RNAwolf: 0.508 RSpredict(seed): 0.346 Positive Predictive Value RNAwolf: 0.508 RSpredict(seed): 0.662 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.6410608252e-08	10 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.660 RSpredict(seed): 0.017 Sensitivity CMfinder(20): 0.580 RSpredict(seed): 0.008 Positive Predictive Value CMfinder(20): 0.759 RSpredict(seed): 0.054 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	18 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.344 RSpredict(seed): 0.106 Sensitivity NanoFolder: 0.434 RSpredict(seed): 0.053 Positive Predictive Value NanoFolder: 0.287 RSpredict(seed): 0.230 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	34 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.630 RSpredict(seed): 0.478 Sensitivity RDfolder: 0.598 RSpredict(seed): 0.326 Positive Predictive Value RDfolder: 0.679 RSpredict(seed): 0.721 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08		- Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.679 RSpredict(seed): 0.341 Sensitivity Multilign(seed): 0.629 RSpredict(seed): 0.209 Positive Predictive Value Multilign(seed): 0.742 RSpredict(seed): 0.574 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.29018360962e-08	+ RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.175 PPfold(seed): 0.157 Sensitivity RSpredict(seed): 0.087 PPfold(seed): 0.040 Positive Predictive Value RSpredict(seed): 0.368 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000114483813978	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.555 Carnac(seed): 0.473 Sensitivity RSpredict(seed): 0.422 Carnac(seed): 0.237 Positive Predictive Value RSpredict(seed): 0.731 Carnac(seed): 0.946 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.316 Mastr(seed): 0.262 Sensitivity RSpredict(seed): 0.179 Mastr(seed): 0.080 Positive Predictive Value RSpredict(seed): 0.572 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 RSpredict(seed): 0.566 Sensitivity PETfold_2.0(seed): 0.806 RSpredict(seed): 0.355 Positive Predictive Value PETfold_2.0(seed): 0.862 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(seed)	6 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Multilign(seed): 0.669 Sensitivity CentroidAlifold(20): 0.569 Multilign(seed): 0.632 Positive Predictive Value CentroidAlifold(20): 0.845 Multilign(seed): 0.717 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.766 Multilign(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.686 Multilign(seed): 0.575 Positive Predictive Value PETfold_pre2.0(seed): 0.861 Multilign(seed): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.601 Multilign(seed): 0.554 Sensitivity ContextFold: 0.569 Multilign(seed): 0.489 Positive Predictive Value ContextFold: 0.645 Multilign(seed): 0.638 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 MXScarna(seed): 0.629 Sensitivity Multilign(seed): 0.591 MXScarna(seed): 0.582 Positive Predictive Value Multilign(seed): 0.724 MXScarna(seed): 0.691 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 RNAalifold(20): 0.708 Sensitivity Multilign(seed): 0.682 RNAalifold(20): 0.651 Positive Predictive Value Multilign(seed): 0.793 RNAalifold(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.553 Multilign(seed): 0.517 Sensitivity PETfold_pre2.0(20): 0.521 Multilign(seed): 0.479 Positive Predictive Value PETfold_pre2.0(20): 0.594 Multilign(seed): 0.565 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs PPfold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 PPfold(20): 0.728 Sensitivity Multilign(seed): 0.682 PPfold(20): 0.643 Positive Predictive Value Multilign(seed): 0.793 PPfold(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.710 Multilign(seed): 0.617 Sensitivity IPknot: 0.632 Multilign(seed): 0.558 Positive Predictive Value IPknot: 0.805 Multilign(seed): 0.693 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.732 MXScarna(20): 0.666 Sensitivity Multilign(seed): 0.682 MXScarna(20): 0.636 Positive Predictive Value Multilign(seed): 0.793 MXScarna(20): 0.707 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.732 RNASampler(20): 0.720 Sensitivity Multilign(seed): 0.682 RNASampler(20): 0.643 Positive Predictive Value Multilign(seed): 0.793 RNASampler(20): 0.814 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.732 TurboFold(20): 0.724 Sensitivity Multilign(seed): 0.682 TurboFold(20): 0.674 Positive Predictive Value Multilign(seed): 0.793 TurboFold(20): 0.784 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 Multilign(seed): 0.679 Sensitivity CentroidAlifold(seed): 0.612 Multilign(seed): 0.629 Positive Predictive Value CentroidAlifold(seed): 0.909 Multilign(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.76606667793e-09	11 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.736 Multilign(seed): 0.679 Sensitivity CentroidFold: 0.680 Multilign(seed): 0.629 Positive Predictive Value CentroidFold: 0.804 Multilign(seed): 0.742 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	8 Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.681 Multilign(seed): 0.649 Sensitivity Sfold: 0.625 Multilign(seed): 0.591 Positive Predictive Value Sfold: 0.751 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.687 Multilign(seed): 0.672 Sensitivity CentroidHomfold‑LAST: 0.654 Multilign(seed): 0.615 Positive Predictive Value CentroidHomfold‑LAST: 0.736 Multilign(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.699 Multilign(seed): 0.649 Sensitivity Contrafold: 0.678 Multilign(seed): 0.591 Positive Predictive Value Contrafold: 0.731 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 RNAalifold(seed): 0.641 Sensitivity Multilign(seed): 0.591 RNAalifold(seed): 0.500 Positive Predictive Value Multilign(seed): 0.724 RNAalifold(seed): 0.832 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.674 Multilign(seed): 0.649 Sensitivity MaxExpect: 0.635 Multilign(seed): 0.591 Positive Predictive Value MaxExpect: 0.725 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.649 HotKnots: 0.581 Sensitivity Multilign(seed): 0.591 HotKnots: 0.596 Positive Predictive Value Multilign(seed): 0.724 HotKnots: 0.579 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.649 UNAFold: 0.578 Sensitivity Multilign(seed): 0.591 UNAFold: 0.577 Positive Predictive Value Multilign(seed): 0.724 UNAFold: 0.591 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.654 Multilign(seed): 0.649 Sensitivity ProbKnot: 0.649 Multilign(seed): 0.591 Positive Predictive Value ProbKnot: 0.668 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Murlet(20): 0.698 Sensitivity Multilign(seed): 0.682 Murlet(20): 0.636 Positive Predictive Value Multilign(seed): 0.793 Murlet(20): 0.774 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.649 PknotsRG: 0.645 Sensitivity Multilign(seed): 0.591 PknotsRG: 0.644 Positive Predictive Value Multilign(seed): 0.724 PknotsRG: 0.657 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.649 RNAfold: 0.642 Sensitivity Multilign(seed): 0.591 RNAfold: 0.644 Positive Predictive Value Multilign(seed): 0.724 RNAfold: 0.650 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.649 RNAshapes: 0.640 Sensitivity Multilign(seed): 0.591 RNAshapes: 0.639 Positive Predictive Value Multilign(seed): 0.724 RNAshapes: 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.649 Fold: 0.604 Sensitivity Multilign(seed): 0.591 Fold: 0.615 Positive Predictive Value Multilign(seed): 0.724 Fold: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.658 Multilign(seed): 0.595 Sensitivity TurboFold(seed): 0.611 Multilign(seed): 0.537 Positive Predictive Value TurboFold(seed): 0.718 Multilign(seed): 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.765 Afold: 0.743 Sensitivity Multilign(seed): 0.710 Afold: 0.720 Positive Predictive Value Multilign(seed): 0.835 Afold: 0.779 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Carnac(20): 0.608 Sensitivity Multilign(seed): 0.682 Carnac(20): 0.434 Positive Predictive Value Multilign(seed): 0.793 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.669 RSpredict(20): 0.523 Sensitivity Multilign(seed): 0.632 RSpredict(20): 0.486 Positive Predictive Value Multilign(seed): 0.717 RSpredict(20): 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.649 RNAsubopt: 0.642 Sensitivity Multilign(seed): 0.591 RNAsubopt: 0.644 Positive Predictive Value Multilign(seed): 0.724 RNAsubopt: 0.650 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.672 Cylofold: 0.605 Sensitivity Multilign(seed): 0.615 Cylofold: 0.559 Positive Predictive Value Multilign(seed): 0.748 Cylofold: 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.661 Multilign(seed): 0.649 Sensitivity McQFold: 0.635 Multilign(seed): 0.591 Positive Predictive Value McQFold: 0.698 Multilign(seed): 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.554 RNASLOpt: 0.454 Sensitivity Multilign(seed): 0.489 RNASLOpt: 0.423 Positive Predictive Value Multilign(seed): 0.638 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.649 Pknots: 0.578 Sensitivity Multilign(seed): 0.591 Pknots: 0.601 Positive Predictive Value Multilign(seed): 0.724 Pknots: 0.568 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 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 Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Multilign(20): 0.768 Sensitivity Multilign(seed): 0.750 Multilign(20): 0.750 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.798 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.696 RNASampler(seed): 0.577 Sensitivity Multilign(seed): 0.649 RNASampler(seed): 0.444 Positive Predictive Value Multilign(seed): 0.754 RNASampler(seed): 0.761 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.702 Multilign(seed): 0.668 Sensitivity Alterna: 0.685 Multilign(seed): 0.629 Positive Predictive Value Alterna: 0.735 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.732 Mastr(20): 0.616 Sensitivity Multilign(seed): 0.682 Mastr(20): 0.488 Positive Predictive Value Multilign(seed): 0.793 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.737 Vsfold4: 0.555 Sensitivity Multilign(seed): 0.689 Vsfold4: 0.530 Positive Predictive Value Multilign(seed): 0.800 Vsfold4: 0.602 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Murlet(seed): 0.516 Sensitivity Multilign(seed): 0.591 Murlet(seed): 0.356 Positive Predictive Value Multilign(seed): 0.724 Murlet(seed): 0.763 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.574 MCFold: 0.476 Sensitivity Multilign(seed): 0.524 MCFold: 0.508 Positive Predictive Value Multilign(seed): 0.638 MCFold: 0.459 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.672 Vsfold5: 0.465 Sensitivity Multilign(seed): 0.615 Vsfold5: 0.453 Positive Predictive Value Multilign(seed): 0.748 Vsfold5: 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.658 RNAwolf: 0.452 Sensitivity Multilign(seed): 0.608 RNAwolf: 0.458 Positive Predictive Value Multilign(seed): 0.721 RNAwolf: 0.461 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	0 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.660 NanoFolder: 0.333 Sensitivity Multilign(seed): 0.600 NanoFolder: 0.375 Positive Predictive Value Multilign(seed): 0.738 NanoFolder: 0.323 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.737 RDfolder: 0.483 Sensitivity Multilign(seed): 0.689 RDfolder: 0.430 Positive Predictive Value Multilign(seed): 0.800 RDfolder: 0.565 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	11 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.679 RSpredict(seed): 0.341 Sensitivity Multilign(seed): 0.629 RSpredict(seed): 0.209 Positive Predictive Value Multilign(seed): 0.742 RSpredict(seed): 0.574 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.29018360962e-08		? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.617 PPfold(seed): 0.152 Sensitivity Multilign(seed): 0.558 PPfold(seed): 0.042 Positive Predictive Value Multilign(seed): 0.693 PPfold(seed): 0.571 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Carnac(seed): 0.323 Sensitivity Multilign(seed): 0.591 Carnac(seed): 0.106 Positive Predictive Value Multilign(seed): 0.724 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.591 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.724 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.967 PETfold_2.0(seed): 0.831 Sensitivity Multilign(seed): 0.968 PETfold_2.0(seed): 0.806 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PPfold(seed)	20 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.809 PPfold(seed): 0.053 Sensitivity CentroidAlifold(20): 0.741 PPfold(seed): 0.010 Positive Predictive Value CentroidAlifold(20): 0.888 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.89920829651e-08	24 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.865 PPfold(seed): 0.166 Sensitivity PETfold_pre2.0(seed): 0.823 PPfold(seed): 0.045 Positive Predictive Value PETfold_pre2.0(seed): 0.912 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.767 PPfold(seed): 0.102 Sensitivity ContextFold: 0.719 PPfold(seed): 0.023 Positive Predictive Value ContextFold: 0.823 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.39090039918e-08	19 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.732 PPfold(seed): 0.094 Sensitivity MXScarna(seed): 0.681 PPfold(seed): 0.019 Positive Predictive Value MXScarna(seed): 0.793 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08	14 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.784 PPfold(seed): 0.046 Sensitivity RNAalifold(20): 0.721 PPfold(seed): 0.009 Positive Predictive Value RNAalifold(20): 0.858 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	17 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.786 PPfold(seed): 0.058 Sensitivity PETfold_pre2.0(20): 0.768 PPfold(seed): 0.012 Positive Predictive Value PETfold_pre2.0(20): 0.808 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	14 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.819 PPfold(seed): 0.046 Sensitivity PPfold(20): 0.766 PPfold(seed): 0.009 Positive Predictive Value PPfold(20): 0.879 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.71568867205e-08	19 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.739 PPfold(seed): 0.094 Sensitivity IPknot: 0.696 PPfold(seed): 0.019 Positive Predictive Value IPknot: 0.791 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	14 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.707 PPfold(seed): 0.046 Sensitivity MXScarna(20): 0.667 PPfold(seed): 0.009 Positive Predictive Value MXScarna(20): 0.757 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	14 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.729 PPfold(seed): 0.046 Sensitivity RNASampler(20): 0.655 PPfold(seed): 0.009 Positive Predictive Value RNASampler(20): 0.819 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	14 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.764 PPfold(seed): 0.046 Sensitivity TurboFold(20): 0.726 PPfold(seed): 0.009 Positive Predictive Value TurboFold(20): 0.810 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.39551335374e-08	27 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 PPfold(seed): 0.157 Sensitivity CentroidAlifold(seed): 0.496 PPfold(seed): 0.040 Positive Predictive Value CentroidAlifold(seed): 0.950 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.703 PPfold(seed): 0.157 Sensitivity CentroidFold: 0.692 PPfold(seed): 0.040 Positive Predictive Value CentroidFold: 0.722 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.658 PPfold(seed): 0.094 Sensitivity Sfold: 0.621 PPfold(seed): 0.019 Positive Predictive Value Sfold: 0.706 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.30295446166e-08	18 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.719 PPfold(seed): 0.091 Sensitivity CentroidHomfold‑LAST: 0.705 PPfold(seed): 0.016 Positive Predictive Value CentroidHomfold‑LAST: 0.741 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	19 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.706 PPfold(seed): 0.094 Sensitivity Contrafold: 0.700 PPfold(seed): 0.019 Positive Predictive Value Contrafold: 0.719 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	11 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.653 PPfold(seed): 0.124 Sensitivity RNAalifold(seed): 0.496 PPfold(seed): 0.034 Positive Predictive Value RNAalifold(seed): 0.868 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	19 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.638 PPfold(seed): 0.094 Sensitivity MaxExpect: 0.623 PPfold(seed): 0.019 Positive Predictive Value MaxExpect: 0.663 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	19 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.617 PPfold(seed): 0.094 Sensitivity HotKnots: 0.636 PPfold(seed): 0.019 Positive Predictive Value HotKnots: 0.609 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	19 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.589 PPfold(seed): 0.094 Sensitivity UNAFold: 0.595 PPfold(seed): 0.019 Positive Predictive Value UNAFold: 0.593 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	19 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.641 PPfold(seed): 0.094 Sensitivity ProbKnot: 0.655 PPfold(seed): 0.019 Positive Predictive Value ProbKnot: 0.638 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.79203144115e-08	14 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.671 PPfold(seed): 0.046 Sensitivity Murlet(20): 0.598 PPfold(seed): 0.009 Positive Predictive Value Murlet(20): 0.761 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	19 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.674 PPfold(seed): 0.094 Sensitivity PknotsRG: 0.685 PPfold(seed): 0.019 Positive Predictive Value PknotsRG: 0.672 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	19 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.653 PPfold(seed): 0.094 Sensitivity RNAfold: 0.657 PPfold(seed): 0.019 Positive Predictive Value RNAfold: 0.657 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	19 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.633 PPfold(seed): 0.094 Sensitivity RNAshapes: 0.638 PPfold(seed): 0.019 Positive Predictive Value RNAshapes: 0.637 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	19 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.625 PPfold(seed): 0.094 Sensitivity Fold: 0.640 PPfold(seed): 0.019 Positive Predictive Value Fold: 0.620 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	10 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.624 PPfold(seed): 0.130 Sensitivity TurboFold(seed): 0.590 PPfold(seed): 0.037 Positive Predictive Value TurboFold(seed): 0.670 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	6 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.632 PPfold(seed): 0.158 Sensitivity Afold: 0.634 PPfold(seed): 0.048 Positive Predictive Value Afold: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	14 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.654 PPfold(seed): 0.046 Sensitivity Carnac(20): 0.516 PPfold(seed): 0.009 Positive Predictive Value Carnac(20): 0.838 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	20 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.627 PPfold(seed): 0.053 Sensitivity RSpredict(20): 0.575 PPfold(seed): 0.010 Positive Predictive Value RSpredict(20): 0.693 PPfold(seed): 0.294 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	19 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.635 PPfold(seed): 0.094 Sensitivity RNAsubopt: 0.647 PPfold(seed): 0.019 Positive Predictive Value RNAsubopt: 0.633 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	16 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.684 PPfold(seed): 0.107 Sensitivity Cylofold: 0.659 PPfold(seed): 0.016 Positive Predictive Value Cylofold: 0.721 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.24519439238e-08	19 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.666 PPfold(seed): 0.094 Sensitivity McQFold: 0.657 PPfold(seed): 0.019 Positive Predictive Value McQFold: 0.684 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	16 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.617 PPfold(seed): 0.102 Sensitivity RNASLOpt: 0.587 PPfold(seed): 0.023 Positive Predictive Value RNASLOpt: 0.657 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.21671975982e-08	19 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.604 PPfold(seed): 0.094 Sensitivity Pknots: 0.625 PPfold(seed): 0.019 Positive Predictive Value Pknots: 0.593 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	9 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 PPfold(seed): 0.134 Sensitivity CRWrnafold: 0.655 PPfold(seed): 0.034 Positive Predictive Value CRWrnafold: 0.649 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	13 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.681 PPfold(seed): 0.023 Sensitivity Multilign(20): 0.671 PPfold(seed): 0.003 Positive Predictive Value Multilign(20): 0.701 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.64686604905e-09	6 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.530 PPfold(seed): 0.164 Sensitivity RNASampler(seed): 0.425 PPfold(seed): 0.059 Positive Predictive Value RNASampler(seed): 0.670 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.671 PPfold(seed): 0.185 Sensitivity Alterna: 0.677 PPfold(seed): 0.047 Positive Predictive Value Alterna: 0.677 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	14 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.616 PPfold(seed): 0.046 Sensitivity Mastr(20): 0.493 PPfold(seed): 0.009 Positive Predictive Value Mastr(20): 0.779 PPfold(seed): 0.273 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	17 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.610 PPfold(seed): 0.094 Sensitivity Vsfold4: 0.593 PPfold(seed): 0.017 Positive Predictive Value Vsfold4: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	11 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.496 PPfold(seed): 0.124 Sensitivity Murlet(seed): 0.337 PPfold(seed): 0.034 Positive Predictive Value Murlet(seed): 0.742 PPfold(seed): 0.474 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.09700314043e-09	22 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.489 PPfold(seed): 0.175 Sensitivity MCFold: 0.538 PPfold(seed): 0.050 Positive Predictive Value MCFold: 0.456 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.513 PPfold(seed): 0.091 Sensitivity Vsfold5: 0.514 PPfold(seed): 0.016 Positive Predictive Value Vsfold5: 0.526 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	27 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.472 PPfold(seed): 0.157 Sensitivity RNAwolf: 0.479 PPfold(seed): 0.040 Positive Predictive Value RNAwolf: 0.478 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.652 PPfold(seed): 0.000 Sensitivity CMfinder(20): 0.518 PPfold(seed): 0.000 Positive Predictive Value CMfinder(20): 0.831 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.338 PPfold(seed): 0.114 Sensitivity NanoFolder: 0.414 PPfold(seed): 0.025 Positive Predictive Value NanoFolder: 0.293 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.16841705202e-08	10 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.422 PPfold(seed): 0.139 Sensitivity RDfolder: 0.375 PPfold(seed): 0.027 Positive Predictive Value RDfolder: 0.497 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	27 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.175 PPfold(seed): 0.157 Sensitivity RSpredict(seed): 0.087 PPfold(seed): 0.040 Positive Predictive Value RSpredict(seed): 0.368 PPfold(seed): 0.634 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000114483813978	7 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.617 PPfold(seed): 0.152 Sensitivity Multilign(seed): 0.558 PPfold(seed): 0.042 Positive Predictive Value Multilign(seed): 0.693 PPfold(seed): 0.571 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		+ PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.117 Carnac(seed): 0.115 Sensitivity PPfold(seed): 0.030 Carnac(seed): 0.013 Positive Predictive Value PPfold(seed): 0.474 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.000163025247502	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.094 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.019 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.474 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.806 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.862 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Carnac(seed)	24 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Carnac(seed): 0.173 Sensitivity CentroidAlifold(20): 0.661 Carnac(seed): 0.030 Positive Predictive Value CentroidAlifold(20): 0.884 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Carnac(seed): 0.562 Sensitivity PETfold_pre2.0(seed): 0.804 Carnac(seed): 0.339 Positive Predictive Value PETfold_pre2.0(seed): 0.867 Carnac(seed): 0.934 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	11 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.805 Carnac(seed): 0.575 Sensitivity ContextFold: 0.779 Carnac(seed): 0.356 Positive Predictive Value ContextFold: 0.833 Carnac(seed): 0.929 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	35 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.784 Carnac(seed): 0.474 Sensitivity MXScarna(seed): 0.750 Carnac(seed): 0.239 Positive Predictive Value MXScarna(seed): 0.820 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.744 Carnac(seed): 0.220 Sensitivity RNAalifold(20): 0.657 Carnac(seed): 0.049 Positive Predictive Value RNAalifold(20): 0.849 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	9 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.633 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.606 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.668 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.723 Carnac(seed): 0.272 Sensitivity PPfold(20): 0.646 Carnac(seed): 0.075 Positive Predictive Value PPfold(20): 0.816 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.10032755566e-08	13 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.726 Carnac(seed): 0.553 Sensitivity IPknot: 0.696 Carnac(seed): 0.330 Positive Predictive Value IPknot: 0.760 Carnac(seed): 0.929 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	23 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.739 Carnac(seed): 0.220 Sensitivity MXScarna(20): 0.702 Carnac(seed): 0.049 Positive Predictive Value MXScarna(20): 0.784 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.742 Carnac(seed): 0.220 Sensitivity RNASampler(20): 0.652 Carnac(seed): 0.049 Positive Predictive Value RNASampler(20): 0.850 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	10 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.718 Carnac(seed): 0.272 Sensitivity TurboFold(20): 0.675 Carnac(seed): 0.075 Positive Predictive Value TurboFold(20): 0.771 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	38 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.804 Carnac(seed): 0.467 Sensitivity CentroidAlifold(seed): 0.715 Carnac(seed): 0.232 Positive Predictive Value CentroidAlifold(seed): 0.905 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.743 Carnac(seed): 0.467 Sensitivity CentroidFold: 0.730 Carnac(seed): 0.232 Positive Predictive Value CentroidFold: 0.758 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.704 Carnac(seed): 0.474 Sensitivity Sfold: 0.690 Carnac(seed): 0.239 Positive Predictive Value Sfold: 0.719 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.660 Carnac(seed): 0.273 Sensitivity CentroidHomfold‑LAST: 0.638 Carnac(seed): 0.076 Positive Predictive Value CentroidHomfold‑LAST: 0.693 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	35 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.738 Carnac(seed): 0.474 Sensitivity Contrafold: 0.747 Carnac(seed): 0.239 Positive Predictive Value Contrafold: 0.731 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	31 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.780 Carnac(seed): 0.499 Sensitivity RNAalifold(seed): 0.680 Carnac(seed): 0.264 Positive Predictive Value RNAalifold(seed): 0.895 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.688 Carnac(seed): 0.473 Sensitivity MaxExpect: 0.694 Carnac(seed): 0.239 Positive Predictive Value MaxExpect: 0.683 Carnac(seed): 0.941 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.732 Carnac(seed): 0.277 Sensitivity HotKnots: 0.751 Carnac(seed): 0.078 Positive Predictive Value HotKnots: 0.722 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.678 Carnac(seed): 0.474 Sensitivity UNAFold: 0.686 Carnac(seed): 0.239 Positive Predictive Value UNAFold: 0.672 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.651 Carnac(seed): 0.486 Sensitivity ProbKnot: 0.663 Carnac(seed): 0.253 Positive Predictive Value ProbKnot: 0.640 Carnac(seed): 0.934 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	23 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.671 Carnac(seed): 0.220 Sensitivity Murlet(20): 0.566 Carnac(seed): 0.049 Positive Predictive Value Murlet(20): 0.802 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	34 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.740 Carnac(seed): 0.277 Sensitivity PknotsRG: 0.753 Carnac(seed): 0.078 Positive Predictive Value PknotsRG: 0.734 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.680 Carnac(seed): 0.474 Sensitivity RNAfold: 0.691 Carnac(seed): 0.239 Positive Predictive Value RNAfold: 0.671 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.751 Carnac(seed): 0.277 Sensitivity RNAshapes: 0.755 Carnac(seed): 0.078 Positive Predictive Value RNAshapes: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.652 Carnac(seed): 0.499 Sensitivity Fold: 0.672 Carnac(seed): 0.266 Positive Predictive Value Fold: 0.635 Carnac(seed): 0.941 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	11 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 Carnac(seed): 0.288 Sensitivity TurboFold(seed): 0.615 Carnac(seed): 0.084 Positive Predictive Value TurboFold(seed): 0.691 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	24 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.774 Carnac(seed): 0.341 Sensitivity Afold: 0.780 Carnac(seed): 0.118 Positive Predictive Value Afold: 0.773 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.672 Carnac(seed): 0.220 Sensitivity Carnac(20): 0.484 Carnac(seed): 0.049 Positive Predictive Value Carnac(20): 0.939 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.89920829651e-08	25 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.572 Carnac(seed): 0.214 Sensitivity RSpredict(20): 0.508 Carnac(seed): 0.046 Positive Predictive Value RSpredict(20): 0.652 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	34 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.718 Carnac(seed): 0.277 Sensitivity RNAsubopt: 0.732 Carnac(seed): 0.078 Positive Predictive Value RNAsubopt: 0.712 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.684 Carnac(seed): 0.216 Sensitivity Cylofold: 0.662 Carnac(seed): 0.047 Positive Predictive Value Cylofold: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.66763272401e-08	35 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.654 Carnac(seed): 0.474 Sensitivity McQFold: 0.656 Carnac(seed): 0.239 Positive Predictive Value McQFold: 0.655 Carnac(seed): 0.942 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.534 Carnac(seed): 0.126 Sensitivity RNASLOpt: 0.512 Carnac(seed): 0.016 Positive Predictive Value RNASLOpt: 0.567 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	34 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.674 Carnac(seed): 0.277 Sensitivity Pknots: 0.709 Carnac(seed): 0.078 Positive Predictive Value Pknots: 0.648 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	7 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 Carnac(seed): 0.156 Sensitivity CRWrnafold: 0.595 Carnac(seed): 0.025 Positive Predictive Value CRWrnafold: 0.591 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.560 Carnac(seed): 0.269 Sensitivity Multilign(20): 0.524 Carnac(seed): 0.073 Positive Predictive Value Multilign(20): 0.611 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.76570236188e-09	19 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Carnac(seed): 0.394 Sensitivity RNASampler(seed): 0.634 Carnac(seed): 0.157 Positive Predictive Value RNASampler(seed): 0.843 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.840 Carnac(seed): 0.420 Sensitivity Alterna: 0.828 Carnac(seed): 0.180 Positive Predictive Value Alterna: 0.860 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.61358433984e-08	23 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.604 Carnac(seed): 0.220 Sensitivity Mastr(20): 0.449 Carnac(seed): 0.049 Positive Predictive Value Mastr(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.616 Carnac(seed): 0.287 Sensitivity Vsfold4: 0.601 Carnac(seed): 0.084 Positive Predictive Value Vsfold4: 0.642 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.594 Carnac(seed): 0.300 Sensitivity Murlet(seed): 0.418 Carnac(seed): 0.091 Positive Predictive Value Murlet(seed): 0.855 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.571 Carnac(seed): 0.324 Sensitivity MCFold: 0.622 Carnac(seed): 0.106 Positive Predictive Value MCFold: 0.535 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.580 Carnac(seed): 0.282 Sensitivity Vsfold5: 0.576 Carnac(seed): 0.081 Positive Predictive Value Vsfold5: 0.595 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.543 RNAwolf: 0.487 Sensitivity Carnac(seed): 0.317 RNAwolf: 0.488 Positive Predictive Value Carnac(seed): 0.934 RNAwolf: 0.488 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.47424713927e-05	1 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.536 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.292 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	6 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.363 Carnac(seed): 0.161 Sensitivity NanoFolder: 0.434 Carnac(seed): 0.026 Positive Predictive Value NanoFolder: 0.319 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	21 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.633 Carnac(seed): 0.374 Sensitivity RDfolder: 0.582 Carnac(seed): 0.143 Positive Predictive Value RDfolder: 0.707 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	39 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.555 Carnac(seed): 0.473 Sensitivity RSpredict(seed): 0.422 Carnac(seed): 0.237 Positive Predictive Value RSpredict(seed): 0.731 Carnac(seed): 0.946 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Carnac(seed): 0.323 Sensitivity Multilign(seed): 0.591 Carnac(seed): 0.106 Positive Predictive Value Multilign(seed): 0.724 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	12 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.117 Carnac(seed): 0.115 Sensitivity PPfold(seed): 0.030 Carnac(seed): 0.013 Positive Predictive Value PPfold(seed): 0.474 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.000163025247502		- Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.354 Carnac(seed): 0.277 Sensitivity Mastr(seed): 0.141 Carnac(seed): 0.078 Positive Predictive Value Mastr(seed): 0.899 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08	? CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.806 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.862 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(seed)	39 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.808 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.728 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.901 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.867 Mastr(seed): 0.042 Sensitivity PETfold_pre2.0(seed): 0.826 Mastr(seed): 0.005 Positive Predictive Value PETfold_pre2.0(seed): 0.913 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	16 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.767 Mastr(seed): 0.000 Sensitivity ContextFold: 0.719 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.823 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	52 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.769 Mastr(seed): 0.282 Sensitivity MXScarna(seed): 0.727 Mastr(seed): 0.089 Positive Predictive Value MXScarna(seed): 0.819 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.790 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.793 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.776 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.815 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.42071836373e-08	15 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.812 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.753 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.880 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.64481516727e-08	19 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.739 Mastr(seed): 0.000 Sensitivity IPknot: 0.696 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.791 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	34 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.755 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.720 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.751 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.663 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.856 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.773 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.737 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.817 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	60 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 Mastr(seed): 0.261 Sensitivity CentroidAlifold(seed): 0.535 Mastr(seed): 0.079 Positive Predictive Value CentroidAlifold(seed): 0.884 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.722 Mastr(seed): 0.261 Sensitivity CentroidFold: 0.725 Mastr(seed): 0.079 Positive Predictive Value CentroidFold: 0.724 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.705 Mastr(seed): 0.279 Sensitivity Sfold: 0.693 Mastr(seed): 0.088 Positive Predictive Value Sfold: 0.723 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.728 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.715 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.749 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	53 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.701 Mastr(seed): 0.279 Sensitivity Contrafold: 0.725 Mastr(seed): 0.088 Positive Predictive Value Contrafold: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.680 Mastr(seed): 0.345 Sensitivity RNAalifold(seed): 0.525 Mastr(seed): 0.134 Positive Predictive Value RNAalifold(seed): 0.885 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.699 Mastr(seed): 0.291 Sensitivity MaxExpect: 0.711 Mastr(seed): 0.095 Positive Predictive Value MaxExpect: 0.692 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.678 Mastr(seed): 0.279 Sensitivity HotKnots: 0.707 Mastr(seed): 0.088 Positive Predictive Value HotKnots: 0.656 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.683 Mastr(seed): 0.279 Sensitivity UNAFold: 0.702 Mastr(seed): 0.088 Positive Predictive Value UNAFold: 0.671 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.663 Mastr(seed): 0.221 Sensitivity ProbKnot: 0.696 Mastr(seed): 0.049 Positive Predictive Value ProbKnot: 0.638 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.693 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.594 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.815 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.693 Mastr(seed): 0.279 Sensitivity PknotsRG: 0.720 Mastr(seed): 0.088 Positive Predictive Value PknotsRG: 0.674 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.693 Mastr(seed): 0.279 Sensitivity RNAfold: 0.716 Mastr(seed): 0.088 Positive Predictive Value RNAfold: 0.676 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.683 Mastr(seed): 0.279 Sensitivity RNAshapes: 0.702 Mastr(seed): 0.088 Positive Predictive Value RNAshapes: 0.672 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.704 Mastr(seed): 0.289 Sensitivity Fold: 0.732 Mastr(seed): 0.095 Positive Predictive Value Fold: 0.683 Mastr(seed): 0.885 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.647 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.615 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.691 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.02510705504e-08	35 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.661 Mastr(seed): 0.344 Sensitivity Afold: 0.691 Mastr(seed): 0.133 Positive Predictive Value Afold: 0.638 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.686 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.915 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.660 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.597 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.735 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.661 Mastr(seed): 0.279 Sensitivity RNAsubopt: 0.690 Mastr(seed): 0.088 Positive Predictive Value RNAsubopt: 0.641 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.706 Mastr(seed): 0.260 Sensitivity Cylofold: 0.693 Mastr(seed): 0.068 Positive Predictive Value Cylofold: 0.729 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	53 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.656 Mastr(seed): 0.279 Sensitivity McQFold: 0.665 Mastr(seed): 0.088 Positive Predictive Value McQFold: 0.654 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.617 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.587 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.657 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.16042554876e-08	51 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.683 Mastr(seed): 0.295 Sensitivity Pknots: 0.716 Mastr(seed): 0.098 Positive Predictive Value Pknots: 0.660 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.655 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.649 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	15 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.652 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.624 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.692 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08	19 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.728 Mastr(seed): 0.503 Sensitivity RNASampler(seed): 0.634 Mastr(seed): 0.285 Positive Predictive Value RNASampler(seed): 0.843 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	29 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.757 Mastr(seed): 0.421 Sensitivity Alterna: 0.765 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.760 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	34 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.620 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.473 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.819 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	51 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.608 Mastr(seed): 0.285 Sensitivity Vsfold4: 0.607 Mastr(seed): 0.092 Positive Predictive Value Vsfold4: 0.617 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.594 Mastr(seed): 0.382 Sensitivity Murlet(seed): 0.418 Mastr(seed): 0.165 Positive Predictive Value Murlet(seed): 0.855 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.557 Mastr(seed): 0.297 Sensitivity MCFold: 0.608 Mastr(seed): 0.103 Positive Predictive Value MCFold: 0.521 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.556 Mastr(seed): 0.282 Sensitivity Vsfold5: 0.561 Mastr(seed): 0.090 Positive Predictive Value Vsfold5: 0.561 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.477 Mastr(seed): 0.040 Sensitivity RNAwolf: 0.484 Mastr(seed): 0.004 Positive Predictive Value RNAwolf: 0.482 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	4 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.652 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.831 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.338 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.414 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.293 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.82838438772e-09	33 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.626 Mastr(seed): 0.390 Sensitivity RDfolder: 0.592 Mastr(seed): 0.173 Positive Predictive Value RDfolder: 0.677 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.316 Mastr(seed): 0.262 Sensitivity RSpredict(seed): 0.179 Mastr(seed): 0.080 Positive Predictive Value RSpredict(seed): 0.572 Mastr(seed): 0.869 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.649 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.591 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.724 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.094 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.019 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.474 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	34 Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.354 Carnac(seed): 0.277 Sensitivity Mastr(seed): 0.141 Carnac(seed): 0.078 Positive Predictive Value Mastr(seed): 0.899 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.85233844192e-08		? Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.845 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.889 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.923 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
CMfinder(seed)	0 CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 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 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 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 CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs 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 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 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 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(seed)	1 PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CentroidAlifold(20): 0.863 Sensitivity PETfold_2.0(seed): 0.889 CentroidAlifold(20): 0.815 Positive Predictive Value PETfold_2.0(seed): 0.923 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.874 PETfold_2.0(seed): 0.866 Sensitivity PETfold_pre2.0(seed): 0.845 PETfold_2.0(seed): 0.845 Positive Predictive Value PETfold_pre2.0(seed): 0.907 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.938 PETfold_2.0(seed): 0.866 Sensitivity ContextFold: 0.914 PETfold_2.0(seed): 0.845 Positive Predictive Value ContextFold: 0.964 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 MXScarna(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient MXScarna(seed): 0.884 PETfold_2.0(seed): 0.866 Sensitivity MXScarna(seed): 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value MXScarna(seed): 0.909 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 RNAalifold(20): 0.863 Sensitivity PETfold_2.0(seed): 0.889 RNAalifold(20): 0.815 Positive Predictive Value PETfold_2.0(seed): 0.923 RNAalifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.905 PETfold_2.0(seed): 0.905 Sensitivity PETfold_pre2.0(20): 0.889 PETfold_2.0(seed): 0.889 Positive Predictive Value PETfold_pre2.0(20): 0.923 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 IPknot: 0.766 Sensitivity PETfold_2.0(seed): 0.845 IPknot: 0.776 Positive Predictive Value PETfold_2.0(seed): 0.891 IPknot: 0.763 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 MXScarna(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient MXScarna(20): 1.000 PETfold_2.0(seed): 0.905 Sensitivity MXScarna(20): 1.000 PETfold_2.0(seed): 0.889 Positive Predictive Value MXScarna(20): 1.000 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 RNASampler(20): 0.881 Sensitivity PETfold_2.0(seed): 0.889 RNASampler(20): 0.778 Positive Predictive Value PETfold_2.0(seed): 0.923 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 CentroidAlifold(seed): 0.756 Sensitivity PETfold_2.0(seed): 0.845 CentroidAlifold(seed): 0.638 Positive Predictive Value PETfold_2.0(seed): 0.891 CentroidAlifold(seed): 0.902 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 CentroidFold: 0.853 Sensitivity PETfold_2.0(seed): 0.845 CentroidFold: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 CentroidFold: 0.847 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Sfold: 0.858 Sensitivity PETfold_2.0(seed): 0.845 Sfold: 0.845 Positive Predictive Value PETfold_2.0(seed): 0.891 Sfold: 0.875 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CentroidHomfold‑LAST: 0.720 Sensitivity PETfold_2.0(seed): 0.889 CentroidHomfold‑LAST: 0.667 Positive Predictive Value PETfold_2.0(seed): 0.923 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Contrafold: 0.853 Sensitivity PETfold_2.0(seed): 0.845 Contrafold: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 Contrafold: 0.847 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 RNAalifold(seed): 0.780 Sensitivity PETfold_2.0(seed): 0.806 RNAalifold(seed): 0.613 Positive Predictive Value PETfold_2.0(seed): 0.862 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 MaxExpect: 0.845 Sensitivity PETfold_2.0(seed): 0.845 MaxExpect: 0.862 Positive Predictive Value PETfold_2.0(seed): 0.891 MaxExpect: 0.833 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 HotKnots vs PETfold_2.0(seed) Matthews Correlation Coefficient HotKnots: 0.868 PETfold_2.0(seed): 0.866 Sensitivity HotKnots: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value HotKnots: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 UNAFold vs PETfold_2.0(seed) Matthews Correlation Coefficient UNAFold: 0.868 PETfold_2.0(seed): 0.866 Sensitivity UNAFold: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value UNAFold: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 ProbKnot: 0.848 Sensitivity PETfold_2.0(seed): 0.845 ProbKnot: 0.879 Positive Predictive Value PETfold_2.0(seed): 0.891 ProbKnot: 0.823 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Murlet(20): 0.881 Sensitivity PETfold_2.0(seed): 0.889 Murlet(20): 0.778 Positive Predictive Value PETfold_2.0(seed): 0.923 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PknotsRG vs PETfold_2.0(seed) Matthews Correlation Coefficient PknotsRG: 0.868 PETfold_2.0(seed): 0.866 Sensitivity PknotsRG: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value PknotsRG: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAfold vs PETfold_2.0(seed) Matthews Correlation Coefficient RNAfold: 0.868 PETfold_2.0(seed): 0.866 Sensitivity RNAfold: 0.862 PETfold_2.0(seed): 0.845 Positive Predictive Value RNAfold: 0.877 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNAshapes: 0.612 Sensitivity PETfold_2.0(seed): 0.845 RNAshapes: 0.638 Positive Predictive Value PETfold_2.0(seed): 0.891 RNAshapes: 0.597 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Fold: 0.855 Sensitivity PETfold_2.0(seed): 0.845 Fold: 0.879 Positive Predictive Value PETfold_2.0(seed): 0.891 Fold: 0.836 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.967 PETfold_2.0(seed): 0.831 Sensitivity TurboFold(seed): 0.968 PETfold_2.0(seed): 0.806 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Carnac(20): 0.815 Sensitivity PETfold_2.0(seed): 0.889 Carnac(20): 0.667 Positive Predictive Value PETfold_2.0(seed): 0.923 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 RNAsubopt vs PETfold_2.0(seed) Matthews Correlation Coefficient RNAsubopt: 0.887 PETfold_2.0(seed): 0.866 Sensitivity RNAsubopt: 0.897 PETfold_2.0(seed): 0.845 Positive Predictive Value RNAsubopt: 0.881 PETfold_2.0(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 McQFold: 0.763 Sensitivity PETfold_2.0(seed): 0.845 McQFold: 0.690 Positive Predictive Value PETfold_2.0(seed): 0.891 McQFold: 0.851 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNASLOpt: 0.776 Sensitivity PETfold_2.0(seed): 0.845 RNASLOpt: 0.759 Positive Predictive Value PETfold_2.0(seed): 0.891 RNASLOpt: 0.800 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Pknots: 0.781 Sensitivity PETfold_2.0(seed): 0.845 Pknots: 0.810 Positive Predictive Value PETfold_2.0(seed): 0.891 Pknots: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Mastr(20): 0.274 Sensitivity PETfold_2.0(seed): 0.889 Mastr(20): 0.259 Positive Predictive Value PETfold_2.0(seed): 0.923 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Vsfold4: 0.193 Sensitivity PETfold_2.0(seed): 0.889 Vsfold4: 0.185 Positive Predictive Value PETfold_2.0(seed): 0.923 Vsfold4: 0.217 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 Murlet(seed): 0.475 Sensitivity PETfold_2.0(seed): 0.806 Murlet(seed): 0.258 Positive Predictive Value PETfold_2.0(seed): 0.862 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 Vsfold5: 0.177 Sensitivity PETfold_2.0(seed): 0.889 Vsfold5: 0.185 Positive Predictive Value PETfold_2.0(seed): 0.923 Vsfold5: 0.185 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 RNAwolf: 0.704 Sensitivity PETfold_2.0(seed): 0.845 RNAwolf: 0.690 Positive Predictive Value PETfold_2.0(seed): 0.891 RNAwolf: 0.727 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 CMfinder(20): 0.526 Sensitivity PETfold_2.0(seed): 0.889 CMfinder(20): 0.407 Positive Predictive Value PETfold_2.0(seed): 0.923 CMfinder(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.905 NanoFolder: 0.281 Sensitivity PETfold_2.0(seed): 0.889 NanoFolder: 0.370 Positive Predictive Value PETfold_2.0(seed): 0.923 NanoFolder: 0.227 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 RSpredict(seed): 0.566 Sensitivity PETfold_2.0(seed): 0.806 RSpredict(seed): 0.355 Positive Predictive Value PETfold_2.0(seed): 0.862 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.967 PETfold_2.0(seed): 0.831 Sensitivity Multilign(seed): 0.968 PETfold_2.0(seed): 0.806 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.806 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.862 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.831 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.806 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.862 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.866 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.845 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 PETfold_2.0(seed): 0.905 Sensitivity PETfold_2.0(20): 0.889 PETfold_2.0(seed): 0.889 Positive Predictive Value PETfold_2.0(20): 0.923 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
DAFS(20)	0 CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(20)	1 PETfold_2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidAlifold(20): 0.863 Sensitivity PETfold_2.0(20): 0.889 CentroidAlifold(20): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.905 PETfold_2.0(20): 0.905 Sensitivity PETfold_pre2.0(seed): 0.889 PETfold_2.0(20): 0.889 Positive Predictive Value PETfold_pre2.0(seed): 0.923 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.981 PETfold_2.0(20): 0.905 Sensitivity ContextFold: 0.963 PETfold_2.0(20): 0.889 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 MXScarna(seed): 0.845 Sensitivity PETfold_2.0(20): 0.889 MXScarna(seed): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 MXScarna(seed): 0.880 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAalifold(20): 0.863 Sensitivity PETfold_2.0(20): 0.889 RNAalifold(20): 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 RNAalifold(20): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.905 PETfold_2.0(20): 0.905 Sensitivity PETfold_pre2.0(20): 0.889 PETfold_2.0(20): 0.889 Positive Predictive Value PETfold_pre2.0(20): 0.923 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.905 IPknot: 0.541 Sensitivity PETfold_2.0(20): 0.889 IPknot: 0.556 Positive Predictive Value PETfold_2.0(20): 0.923 IPknot: 0.536 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 1.000 PETfold_2.0(20): 0.905 Sensitivity MXScarna(20): 1.000 PETfold_2.0(20): 0.889 Positive Predictive Value MXScarna(20): 1.000 PETfold_2.0(20): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNASampler(20): 0.881 Sensitivity PETfold_2.0(20): 0.889 RNASampler(20): 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidAlifold(seed): 0.615 Sensitivity PETfold_2.0(20): 0.889 CentroidAlifold(seed): 0.444 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidAlifold(seed): 0.857 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidFold: 0.725 Sensitivity PETfold_2.0(20): 0.889 CentroidFold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidFold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Sfold: 0.729 Sensitivity PETfold_2.0(20): 0.889 Sfold: 0.704 Positive Predictive Value PETfold_2.0(20): 0.923 Sfold: 0.760 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CentroidHomfold‑LAST: 0.720 Sensitivity PETfold_2.0(20): 0.889 CentroidHomfold‑LAST: 0.667 Positive Predictive Value PETfold_2.0(20): 0.923 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Contrafold: 0.725 Sensitivity PETfold_2.0(20): 0.889 Contrafold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 Contrafold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.905 MaxExpect: 0.712 Sensitivity PETfold_2.0(20): 0.889 MaxExpect: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 MaxExpect: 0.690 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.905 HotKnots: 0.752 Sensitivity PETfold_2.0(20): 0.889 HotKnots: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 HotKnots: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 UNAFold: 0.752 Sensitivity PETfold_2.0(20): 0.889 UNAFold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 UNAFold: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.905 ProbKnot: 0.723 Sensitivity PETfold_2.0(20): 0.889 ProbKnot: 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 ProbKnot: 0.677 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Murlet(20): 0.881 Sensitivity PETfold_2.0(20): 0.889 Murlet(20): 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.905 PknotsRG: 0.752 Sensitivity PETfold_2.0(20): 0.889 PknotsRG: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 PknotsRG: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAfold: 0.752 Sensitivity PETfold_2.0(20): 0.889 RNAfold: 0.741 Positive Predictive Value PETfold_2.0(20): 0.923 RNAfold: 0.769 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAshapes: 0.234 Sensitivity PETfold_2.0(20): 0.889 RNAshapes: 0.259 Positive Predictive Value PETfold_2.0(20): 0.923 RNAshapes: 0.226 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Fold: 0.735 Sensitivity PETfold_2.0(20): 0.889 Fold: 0.778 Positive Predictive Value PETfold_2.0(20): 0.923 Fold: 0.700 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Carnac(20): 0.815 Sensitivity PETfold_2.0(20): 0.889 Carnac(20): 0.667 Positive Predictive Value PETfold_2.0(20): 0.923 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAsubopt: 0.798 Sensitivity PETfold_2.0(20): 0.889 RNAsubopt: 0.815 Positive Predictive Value PETfold_2.0(20): 0.923 RNAsubopt: 0.786 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.905 McQFold: 0.653 Sensitivity PETfold_2.0(20): 0.889 McQFold: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 McQFold: 0.727 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNASLOpt: 0.600 Sensitivity PETfold_2.0(20): 0.889 RNASLOpt: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 RNASLOpt: 0.615 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Pknots: 0.583 Sensitivity PETfold_2.0(20): 0.889 Pknots: 0.630 Positive Predictive Value PETfold_2.0(20): 0.923 Pknots: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Mastr(20): 0.274 Sensitivity PETfold_2.0(20): 0.889 Mastr(20): 0.259 Positive Predictive Value PETfold_2.0(20): 0.923 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Vsfold4: 0.193 Sensitivity PETfold_2.0(20): 0.889 Vsfold4: 0.185 Positive Predictive Value PETfold_2.0(20): 0.923 Vsfold4: 0.217 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Vsfold5: 0.177 Sensitivity PETfold_2.0(20): 0.889 Vsfold5: 0.185 Positive Predictive Value PETfold_2.0(20): 0.923 Vsfold5: 0.185 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.905 RNAwolf: 0.588 Sensitivity PETfold_2.0(20): 0.889 RNAwolf: 0.593 Positive Predictive Value PETfold_2.0(20): 0.923 RNAwolf: 0.593 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 CMfinder(20): 0.526 Sensitivity PETfold_2.0(20): 0.889 CMfinder(20): 0.407 Positive Predictive Value PETfold_2.0(20): 0.923 CMfinder(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.905 NanoFolder: 0.281 Sensitivity PETfold_2.0(20): 0.889 NanoFolder: 0.370 Positive Predictive Value PETfold_2.0(20): 0.923 NanoFolder: 0.227 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.889 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.923 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.905 PETfold_2.0(seed): 0.905 Sensitivity PETfold_2.0(20): 0.889 PETfold_2.0(seed): 0.889 Positive Predictive Value PETfold_2.0(20): 0.923 PETfold_2.0(seed): 0.923 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
DAFS(seed)	0 DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A

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

All RNAs from the PDB datasetstandard base pair definition

Summary of pairwise comparisons

Detailed results of pairwise comparisons between methods

All RNAs from the PDB dataset
standard base pair definition