CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Pseudoknotted RNAs from RNAStrand dataset

	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Number of RNA sequences: 919
Robustness test: no

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 21) of the comparisons were based on at least 10 predictions for common targets).

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

Summary of pairwise comparisons

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	PETfold_pre2.0(seed)	no	48	3	0	2	610	610
2	ContextFold	yes	45	4	2	2	919	919
3	CentroidAlifold(seed)	yes	44	6	1	2	610	358
4	CentroidHomfold‑LAST	yes	41	10	0	2	919	627
5	TurboFold(20)	no	38	2	0	13	286	209
6	PETfold_pre2.0(20)	no	37	3	0	13	286	286
7	PPfold(20)	yes	36	4	0	13	286	208
8	Cylofold	no	35	0	0	18	919	47
9	CentroidAlifold(20)	yes	34	6	0	13	286	286
10	IPknot	yes	34	16	1	2	919	909
11	Pknots	no	33	2	1	17	919	46
12	MXScarna(seed)	no	33	18	0	2	610	363
13	RNAalifold(20)	no	32	8	0	13	286	286
14	CentroidFold	yes	31	20	0	2	919	862
15	RNASampler(seed)	no	30	6	0	17	610	13
16	Multilign(20)	no	30	9	1	13	286	196
17	RNAalifold(seed)	no	30	20	1	2	610	363
18	MXScarna(20)	no	27	13	0	13	286	286
18	RNASampler(20)	no	27	13	0	13	286	50
20	Contrafold	yes	27	22	2	2	919	910
21	Murlet(20)	yes	26	14	0	13	286	159
22	Sfold	no	25	25	1	2	919	910
23	ProbKnot	yes	25	26	0	2	919	910
24	MaxExpect	yes	24	26	1	2	919	910
25	McQFold	yes	23	28	0	2	919	669
26	Murlet(seed)	yes	22	14	0	17	610	14
27	Fold	no	22	27	2	2	919	910
28	PknotsRG	no	22	29	0	2	919	818
29	UNAFold	no	21	30	0	2	919	919
30	TurboFold(seed)	no	20	6	1	26	610	10
31	RNAsubopt	no	20	31	0	2	919	627
32	Afold	no	18	32	0	3	919	595
33	RNASLOpt	no	18	32	1	2	919	534
34	RNAfold	no	18	33	0	2	919	910
35	HotKnots	no	17	14	5	17	919	53
36	RDfolder	no	17	15	4	17	919	46
37	CMfinder(20)	yes	14	26	0	13	286	209
38	RNAshapes	no	14	37	0	2	919	579
39	CRWrnafold	yes	13	37	1	2	919	790
40	Carnac(20)	no	12	27	1	13	286	286
41	Vsfold5	no	12	39	0	2	919	591
42	Vsfold4	no	11	40	0	2	919	600
43	RNAwolf	yes	10	40	1	2	919	740
44	CMfinder(seed)	yes	6	27	1	19	610	26
45	Carnac(seed)	no	5	31	1	16	610	62
46	RSpredict(20)	no	5	34	1	13	286	286
47	Alterna	no	3	32	1	17	919	46
48	NanoFolder	yes	3	37	0	13	919	112
49	RSpredict(seed)	no	3	47	1	2	610	354
50	Mastr(20)	yes	2	38	0	13	286	236
51	Mastr(seed)	yes	1	50	0	2	610	278
52	MCFold	yes	0	35	0	18	919	48
N/A	Multilign(seed)	no	0	0	0	53	610	8
N/A	PPfold(seed)	yes	0	0	0	53	610	8

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.


PETfold_pre2.0(seed)		- ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.730 PETfold_pre2.0(seed): 0.717 Sensitivity ContextFold: 0.688 PETfold_pre2.0(seed): 0.651 Positive Predictive Value ContextFold: 0.776 PETfold_pre2.0(seed): 0.790 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.762 CentroidAlifold(seed): 0.746 Sensitivity PETfold_pre2.0(seed): 0.703 CentroidAlifold(seed): 0.615 Positive Predictive Value PETfold_pre2.0(seed): 0.826 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 CentroidHomfold‑LAST: 0.651 Sensitivity PETfold_pre2.0(seed): 0.592 CentroidHomfold‑LAST: 0.483 Positive Predictive Value PETfold_pre2.0(seed): 0.788 CentroidHomfold‑LAST: 0.879 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 TurboFold(20): 0.741 Sensitivity PETfold_pre2.0(seed): 0.674 TurboFold(20): 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.845 TurboFold(20): 0.802 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 PETfold_pre2.0(20): 0.730 Sensitivity PETfold_pre2.0(seed): 0.709 PETfold_pre2.0(20): 0.681 Positive Predictive Value PETfold_pre2.0(seed): 0.810 PETfold_pre2.0(20): 0.783 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 PPfold(20): 0.736 Sensitivity PETfold_pre2.0(seed): 0.682 PPfold(20): 0.641 Positive Predictive Value PETfold_pre2.0(seed): 0.840 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.809 PETfold_pre2.0(seed): 0.737 Sensitivity Cylofold: 0.782 PETfold_pre2.0(seed): 0.666 Positive Predictive Value Cylofold: 0.841 PETfold_pre2.0(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 CentroidAlifold(20): 0.723 Sensitivity PETfold_pre2.0(seed): 0.709 CentroidAlifold(20): 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.810 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 IPknot: 0.573 Sensitivity PETfold_pre2.0(seed): 0.651 IPknot: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.790 IPknot: 0.646 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: 0.781 PETfold_pre2.0(seed): 0.736 Sensitivity Pknots: 0.760 PETfold_pre2.0(seed): 0.661 Positive Predictive Value Pknots: 0.808 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.762 MXScarna(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.703 MXScarna(seed): 0.533 Positive Predictive Value PETfold_pre2.0(seed): 0.826 MXScarna(seed): 0.741 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 RNAalifold(20): 0.668 Sensitivity PETfold_pre2.0(seed): 0.709 RNAalifold(20): 0.588 Positive Predictive Value PETfold_pre2.0(seed): 0.810 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.718 CentroidFold: 0.537 Sensitivity PETfold_pre2.0(seed): 0.652 CentroidFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.791 CentroidFold: 0.607 Number of pairs reference - predicted secondary structure: 609 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 RNASampler(seed): 0.655 Sensitivity PETfold_pre2.0(seed): 0.572 RNASampler(seed): 0.572 Positive Predictive Value PETfold_pre2.0(seed): 0.769 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000309992208728	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.753 Multilign(20): 0.651 Sensitivity PETfold_pre2.0(seed): 0.673 Multilign(20): 0.591 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 RNAalifold(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.700 RNAalifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.820 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNASampler(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.592 RNASampler(20): 0.434 Positive Predictive Value PETfold_pre2.0(seed): 0.783 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 MXScarna(20): 0.608 Sensitivity PETfold_pre2.0(seed): 0.709 MXScarna(20): 0.550 Positive Predictive Value PETfold_pre2.0(seed): 0.810 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Contrafold: 0.520 Sensitivity PETfold_pre2.0(seed): 0.651 Contrafold: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.752 Murlet(20): 0.566 Sensitivity PETfold_pre2.0(seed): 0.683 Murlet(20): 0.445 Positive Predictive Value PETfold_pre2.0(seed): 0.828 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Sfold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.651 Sfold: 0.432 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Sfold: 0.544 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 ProbKnot: 0.472 Sensitivity PETfold_pre2.0(seed): 0.651 ProbKnot: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.790 ProbKnot: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 MaxExpect: 0.476 Sensitivity PETfold_pre2.0(seed): 0.651 MaxExpect: 0.463 Positive Predictive Value PETfold_pre2.0(seed): 0.790 MaxExpect: 0.489 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 McQFold: 0.455 Sensitivity PETfold_pre2.0(seed): 0.590 McQFold: 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.787 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.791 Murlet(seed): 0.584 Sensitivity PETfold_pre2.0(seed): 0.737 Murlet(seed): 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.849 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Fold: 0.449 Sensitivity PETfold_pre2.0(seed): 0.651 Fold: 0.451 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Fold: 0.447 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.732 PknotsRG: 0.462 Sensitivity PETfold_pre2.0(seed): 0.659 PknotsRG: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.812 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 UNAFold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.651 UNAFold: 0.445 Positive Predictive Value PETfold_pre2.0(seed): 0.790 UNAFold: 0.452 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.650 TurboFold(seed): 0.633 Sensitivity PETfold_pre2.0(seed): 0.584 TurboFold(seed): 0.562 Positive Predictive Value PETfold_pre2.0(seed): 0.727 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71508538796e-06	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 RNAsubopt: 0.468 Sensitivity PETfold_pre2.0(seed): 0.592 RNAsubopt: 0.474 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RNAsubopt: 0.464 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 Afold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.680 Afold: 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.800 Afold: 0.452 Number of pairs reference - predicted secondary structure: 375 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 RNASLOpt: 0.449 Sensitivity PETfold_pre2.0(seed): 0.607 RNASLOpt: 0.424 Positive Predictive Value PETfold_pre2.0(seed): 0.794 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 457 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 RNAfold: 0.439 Sensitivity PETfold_pre2.0(seed): 0.651 RNAfold: 0.440 Positive Predictive Value PETfold_pre2.0(seed): 0.790 RNAfold: 0.439 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 HotKnots: 0.575 Sensitivity PETfold_pre2.0(seed): 0.649 HotKnots: 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.824 HotKnots: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 RDfolder: 0.586 Sensitivity PETfold_pre2.0(seed): 0.661 RDfolder: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.823 RDfolder: 0.682 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(seed): 0.674 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.684 RNAshapes: 0.399 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.394 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAshapes: 0.405 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CRWrnafold: 0.437 Sensitivity PETfold_pre2.0(seed): 0.636 CRWrnafold: 0.437 Positive Predictive Value PETfold_pre2.0(seed): 0.804 CRWrnafold: 0.439 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 Carnac(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.709 Carnac(20): 0.277 Positive Predictive Value PETfold_pre2.0(seed): 0.810 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold5: 0.327 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold5: 0.310 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold5: 0.347 Number of pairs reference - predicted secondary structure: 503 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold4: 0.332 Sensitivity PETfold_pre2.0(seed): 0.595 Vsfold4: 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Vsfold4: 0.364 Number of pairs reference - predicted secondary structure: 509 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAwolf: 0.341 Sensitivity PETfold_pre2.0(seed): 0.590 RNAwolf: 0.356 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAwolf: 0.329 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.457 CMfinder(seed): 0.363 Sensitivity PETfold_pre2.0(seed): 0.309 CMfinder(seed): 0.184 Positive Predictive Value PETfold_pre2.0(seed): 0.678 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.654 Carnac(seed): 0.253 Sensitivity PETfold_pre2.0(seed): 0.534 Carnac(seed): 0.068 Positive Predictive Value PETfold_pre2.0(seed): 0.802 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 RSpredict(20): 0.425 Sensitivity PETfold_pre2.0(seed): 0.709 RSpredict(20): 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.810 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Alterna: 0.503 Sensitivity PETfold_pre2.0(seed): 0.661 Alterna: 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.823 Alterna: 0.543 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.692 NanoFolder: 0.178 Sensitivity PETfold_pre2.0(seed): 0.598 NanoFolder: 0.210 Positive Predictive Value PETfold_pre2.0(seed): 0.801 NanoFolder: 0.153 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.760 RSpredict(seed): 0.363 Sensitivity PETfold_pre2.0(seed): 0.700 RSpredict(seed): 0.222 Positive Predictive Value PETfold_pre2.0(seed): 0.826 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 Mastr(20): 0.035 Sensitivity PETfold_pre2.0(seed): 0.649 Mastr(20): 0.002 Positive Predictive Value PETfold_pre2.0(seed): 0.777 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.714 Mastr(seed): 0.040 Sensitivity PETfold_pre2.0(seed): 0.629 Mastr(seed): 0.002 Positive Predictive Value PETfold_pre2.0(seed): 0.812 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.619 Multilign(seed): 0.575 Sensitivity PETfold_pre2.0(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.721 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 PETfold_pre2.0(seed): 0.619 Sensitivity PPfold(seed): 0.536 PETfold_pre2.0(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 PETfold_pre2.0(seed): 0.721 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 MCFold: 0.336 Sensitivity PETfold_pre2.0(seed): 0.663 MCFold: 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.829 MCFold: 0.303 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.36130997681e-08
ContextFold	610 ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.730 PETfold_pre2.0(seed): 0.717 Sensitivity ContextFold: 0.688 PETfold_pre2.0(seed): 0.651 Positive Predictive Value ContextFold: 0.776 PETfold_pre2.0(seed): 0.790 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.816 CentroidAlifold(seed): 0.746 Sensitivity ContextFold: 0.770 CentroidAlifold(seed): 0.615 Positive Predictive Value ContextFold: 0.864 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.726 CentroidHomfold‑LAST: 0.638 Sensitivity ContextFold: 0.683 CentroidHomfold‑LAST: 0.468 Positive Predictive Value ContextFold: 0.773 CentroidHomfold‑LAST: 0.870 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.840 TurboFold(20): 0.741 Sensitivity ContextFold: 0.791 TurboFold(20): 0.685 Positive Predictive Value ContextFold: 0.892 TurboFold(20): 0.802 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.767 PETfold_pre2.0(20): 0.730 Sensitivity ContextFold: 0.726 PETfold_pre2.0(20): 0.681 Positive Predictive Value ContextFold: 0.811 PETfold_pre2.0(20): 0.783 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.829 PPfold(20): 0.736 Sensitivity ContextFold: 0.780 PPfold(20): 0.641 Positive Predictive Value ContextFold: 0.881 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs ContextFold Matthews Correlation Coefficient Cylofold: 0.701 ContextFold: 0.566 Sensitivity Cylofold: 0.673 ContextFold: 0.505 Positive Predictive Value Cylofold: 0.734 ContextFold: 0.640 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.767 CentroidAlifold(20): 0.723 Sensitivity ContextFold: 0.726 CentroidAlifold(20): 0.595 Positive Predictive Value ContextFold: 0.811 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.678 IPknot: 0.538 Sensitivity ContextFold: 0.636 IPknot: 0.470 Positive Predictive Value ContextFold: 0.724 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs ContextFold Matthews Correlation Coefficient Pknots: 0.697 ContextFold: 0.500 Sensitivity Pknots: 0.668 ContextFold: 0.441 Positive Predictive Value Pknots: 0.733 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.815 MXScarna(seed): 0.628 Sensitivity ContextFold: 0.769 MXScarna(seed): 0.533 Positive Predictive Value ContextFold: 0.864 MXScarna(seed): 0.741 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.767 RNAalifold(20): 0.668 Sensitivity ContextFold: 0.726 RNAalifold(20): 0.588 Positive Predictive Value ContextFold: 0.811 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.699 CentroidFold: 0.505 Sensitivity ContextFold: 0.657 CentroidFold: 0.441 Positive Predictive Value ContextFold: 0.744 CentroidFold: 0.579 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.655 ContextFold: 0.504 Sensitivity RNASampler(seed): 0.572 ContextFold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.841 Multilign(20): 0.651 Sensitivity ContextFold: 0.793 Multilign(20): 0.591 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.804 RNAalifold(seed): 0.629 Sensitivity ContextFold: 0.759 RNAalifold(seed): 0.485 Positive Predictive Value ContextFold: 0.852 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.737 RNASampler(20): 0.553 Sensitivity ContextFold: 0.684 RNASampler(20): 0.434 Positive Predictive Value ContextFold: 0.795 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.767 MXScarna(20): 0.608 Sensitivity ContextFold: 0.726 MXScarna(20): 0.550 Positive Predictive Value ContextFold: 0.811 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.676 Contrafold: 0.496 Sensitivity ContextFold: 0.634 Contrafold: 0.477 Positive Predictive Value ContextFold: 0.722 Contrafold: 0.515 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.805 Murlet(20): 0.566 Sensitivity ContextFold: 0.758 Murlet(20): 0.445 Positive Predictive Value ContextFold: 0.855 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.676 Sfold: 0.451 Sensitivity ContextFold: 0.634 Sfold: 0.400 Positive Predictive Value ContextFold: 0.722 Sfold: 0.509 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.676 ProbKnot: 0.442 Sensitivity ContextFold: 0.634 ProbKnot: 0.437 Positive Predictive Value ContextFold: 0.722 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.676 MaxExpect: 0.447 Sensitivity ContextFold: 0.634 MaxExpect: 0.435 Positive Predictive Value ContextFold: 0.722 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.712 McQFold: 0.450 Sensitivity ContextFold: 0.670 McQFold: 0.440 Positive Predictive Value ContextFold: 0.757 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.697 Murlet(seed): 0.584 Sensitivity ContextFold: 0.636 Murlet(seed): 0.492 Positive Predictive Value ContextFold: 0.765 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.21563533328e-09	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.676 Fold: 0.417 Sensitivity ContextFold: 0.634 Fold: 0.421 Positive Predictive Value ContextFold: 0.722 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.734 PknotsRG: 0.428 Sensitivity ContextFold: 0.689 PknotsRG: 0.427 Positive Predictive Value ContextFold: 0.783 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.672 UNAFold: 0.414 Sensitivity ContextFold: 0.631 UNAFold: 0.412 Positive Predictive Value ContextFold: 0.716 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 919 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.633 ContextFold: 0.602 Sensitivity TurboFold(seed): 0.562 ContextFold: 0.554 Positive Predictive Value TurboFold(seed): 0.716 ContextFold: 0.658 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.23631009584e-09	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.726 RNAsubopt: 0.473 Sensitivity ContextFold: 0.683 RNAsubopt: 0.480 Positive Predictive Value ContextFold: 0.773 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.692 Afold: 0.408 Sensitivity ContextFold: 0.648 Afold: 0.406 Positive Predictive Value ContextFold: 0.739 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.729 RNASLOpt: 0.445 Sensitivity ContextFold: 0.684 RNASLOpt: 0.419 Positive Predictive Value ContextFold: 0.777 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.676 RNAfold: 0.407 Sensitivity ContextFold: 0.634 RNAfold: 0.408 Positive Predictive Value ContextFold: 0.722 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	= HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.453 ContextFold: 0.447 Sensitivity HotKnots: 0.445 ContextFold: 0.407 Positive Predictive Value HotKnots: 0.469 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.282238742299	= RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: 0.508 ContextFold: 0.500 Sensitivity RDfolder: 0.432 ContextFold: 0.441 Positive Predictive Value RDfolder: 0.609 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00456661807577	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.840 CMfinder(20): 0.482 Sensitivity ContextFold: 0.791 CMfinder(20): 0.310 Positive Predictive Value ContextFold: 0.892 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.730 RNAshapes: 0.408 Sensitivity ContextFold: 0.685 RNAshapes: 0.404 Positive Predictive Value ContextFold: 0.778 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.725 CRWrnafold: 0.395 Sensitivity ContextFold: 0.679 CRWrnafold: 0.398 Positive Predictive Value ContextFold: 0.773 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.767 Carnac(20): 0.496 Sensitivity ContextFold: 0.726 Carnac(20): 0.277 Positive Predictive Value ContextFold: 0.811 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.729 Vsfold5: 0.333 Sensitivity ContextFold: 0.685 Vsfold5: 0.317 Positive Predictive Value ContextFold: 0.777 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.726 Vsfold4: 0.337 Sensitivity ContextFold: 0.683 Vsfold4: 0.310 Positive Predictive Value ContextFold: 0.773 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.715 RNAwolf: 0.302 Sensitivity ContextFold: 0.670 RNAwolf: 0.316 Positive Predictive Value ContextFold: 0.764 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.678 CMfinder(seed): 0.363 Sensitivity ContextFold: 0.632 CMfinder(seed): 0.184 Positive Predictive Value ContextFold: 0.729 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.677 Carnac(seed): 0.253 Sensitivity ContextFold: 0.640 Carnac(seed): 0.068 Positive Predictive Value ContextFold: 0.716 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.767 RSpredict(20): 0.425 Sensitivity ContextFold: 0.726 RSpredict(20): 0.345 Positive Predictive Value ContextFold: 0.811 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.500 Alterna: 0.393 Sensitivity ContextFold: 0.441 Alterna: 0.365 Positive Predictive Value ContextFold: 0.577 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.756 NanoFolder: 0.174 Sensitivity ContextFold: 0.712 NanoFolder: 0.207 Positive Predictive Value ContextFold: 0.804 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.814 RSpredict(seed): 0.363 Sensitivity ContextFold: 0.768 RSpredict(seed): 0.222 Positive Predictive Value ContextFold: 0.863 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.694 Mastr(20): 0.035 Sensitivity ContextFold: 0.654 Mastr(20): 0.002 Positive Predictive Value ContextFold: 0.736 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.790 Mastr(seed): 0.040 Sensitivity ContextFold: 0.744 Mastr(seed): 0.002 Positive Predictive Value ContextFold: 0.839 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.575 ContextFold: 0.566 Sensitivity Multilign(seed): 0.536 ContextFold: 0.514 Positive Predictive Value Multilign(seed): 0.625 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): 0.666 ContextFold: 0.566 Sensitivity PPfold(seed): 0.536 ContextFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.449 MCFold: 0.290 Sensitivity ContextFold: 0.402 MCFold: 0.320 Positive Predictive Value ContextFold: 0.511 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	358 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.762 CentroidAlifold(seed): 0.746 Sensitivity PETfold_pre2.0(seed): 0.703 CentroidAlifold(seed): 0.615 Positive Predictive Value PETfold_pre2.0(seed): 0.826 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.816 CentroidAlifold(seed): 0.746 Sensitivity ContextFold: 0.770 CentroidAlifold(seed): 0.615 Positive Predictive Value ContextFold: 0.864 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 CentroidHomfold‑LAST: 0.675 Sensitivity CentroidAlifold(seed): 0.524 CentroidHomfold‑LAST: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.920 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 290 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 CentroidAlifold(seed): 0.723 Sensitivity TurboFold(20): 0.703 CentroidAlifold(seed): 0.550 Positive Predictive Value TurboFold(20): 0.824 CentroidAlifold(seed): 0.952 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.774 CentroidAlifold(seed): 0.770 Sensitivity PETfold_pre2.0(20): 0.725 CentroidAlifold(seed): 0.647 Positive Predictive Value PETfold_pre2.0(20): 0.827 CentroidAlifold(seed): 0.917 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.760 CentroidAlifold(seed): 0.737 Sensitivity PPfold(20): 0.668 CentroidAlifold(seed): 0.573 Positive Predictive Value PPfold(20): 0.864 CentroidAlifold(seed): 0.948 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 CentroidAlifold(seed): 0.780 Sensitivity Cylofold: 0.772 CentroidAlifold(seed): 0.646 Positive Predictive Value Cylofold: 0.828 CentroidAlifold(seed): 0.946 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.17043147862e-08	+ CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 CentroidAlifold(20): 0.765 Sensitivity CentroidAlifold(seed): 0.647 CentroidAlifold(20): 0.646 Positive Predictive Value CentroidAlifold(seed): 0.917 CentroidAlifold(20): 0.906 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 IPknot: 0.611 Sensitivity CentroidAlifold(seed): 0.615 IPknot: 0.536 Positive Predictive Value CentroidAlifold(seed): 0.906 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Pknots: 0.768 Sensitivity CentroidAlifold(seed): 0.642 Pknots: 0.748 Positive Predictive Value CentroidAlifold(seed): 0.936 Pknots: 0.792 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.453544033954	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 MXScarna(seed): 0.628 Sensitivity CentroidAlifold(seed): 0.615 MXScarna(seed): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.906 MXScarna(seed): 0.740 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 RNAalifold(20): 0.722 Sensitivity CentroidAlifold(seed): 0.647 RNAalifold(20): 0.638 Positive Predictive Value CentroidAlifold(seed): 0.917 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 CentroidFold: 0.575 Sensitivity CentroidAlifold(seed): 0.618 CentroidFold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.907 CentroidFold: 0.656 Number of pairs reference - predicted secondary structure: 357 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 RNASampler(seed): 0.655 Sensitivity CentroidAlifold(seed): 0.579 RNASampler(seed): 0.572 Positive Predictive Value CentroidAlifold(seed): 0.902 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Multilign(20): 0.658 Sensitivity CentroidAlifold(seed): 0.546 Multilign(20): 0.595 Positive Predictive Value CentroidAlifold(seed): 0.953 Multilign(20): 0.730 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 RNAalifold(seed): 0.636 Sensitivity CentroidAlifold(seed): 0.615 RNAalifold(seed): 0.490 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAalifold(seed): 0.827 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.702 RNASampler(20): 0.526 Sensitivity CentroidAlifold(seed): 0.526 RNASampler(20): 0.384 Positive Predictive Value CentroidAlifold(seed): 0.939 RNASampler(20): 0.723 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 MXScarna(20): 0.649 Sensitivity CentroidAlifold(seed): 0.647 MXScarna(20): 0.580 Positive Predictive Value CentroidAlifold(seed): 0.917 MXScarna(20): 0.727 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Contrafold: 0.558 Sensitivity CentroidAlifold(seed): 0.615 Contrafold: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.906 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.737 Murlet(20): 0.566 Sensitivity CentroidAlifold(seed): 0.583 Murlet(20): 0.437 Positive Predictive Value CentroidAlifold(seed): 0.933 Murlet(20): 0.734 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Sfold: 0.535 Sensitivity CentroidAlifold(seed): 0.615 Sfold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.906 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 ProbKnot: 0.509 Sensitivity CentroidAlifold(seed): 0.615 ProbKnot: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 MaxExpect: 0.513 Sensitivity CentroidAlifold(seed): 0.615 MaxExpect: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.906 MaxExpect: 0.532 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 McQFold: 0.484 Sensitivity CentroidAlifold(seed): 0.522 McQFold: 0.463 Positive Predictive Value CentroidAlifold(seed): 0.919 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 294 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Murlet(seed): 0.584 Sensitivity CentroidAlifold(seed): 0.718 Murlet(seed): 0.492 Positive Predictive Value CentroidAlifold(seed): 0.915 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Fold: 0.480 Sensitivity CentroidAlifold(seed): 0.615 Fold: 0.477 Positive Predictive Value CentroidAlifold(seed): 0.906 Fold: 0.484 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.763 PknotsRG: 0.488 Sensitivity CentroidAlifold(seed): 0.636 PknotsRG: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.915 PknotsRG: 0.497 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 UNAFold: 0.497 Sensitivity CentroidAlifold(seed): 0.615 UNAFold: 0.487 Positive Predictive Value CentroidAlifold(seed): 0.906 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 TurboFold(seed): 0.633 Sensitivity CentroidAlifold(seed): 0.584 TurboFold(seed): 0.562 Positive Predictive Value CentroidAlifold(seed): 0.883 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.20029949774e-10	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 RNAsubopt: 0.534 Sensitivity CentroidAlifold(seed): 0.524 RNAsubopt: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.920 RNAsubopt: 0.538 Number of pairs reference - predicted secondary structure: 290 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 Afold: 0.483 Sensitivity CentroidAlifold(seed): 0.620 Afold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.907 Afold: 0.493 Number of pairs reference - predicted secondary structure: 306 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNASLOpt: 0.477 Sensitivity CentroidAlifold(seed): 0.540 RNASLOpt: 0.439 Positive Predictive Value CentroidAlifold(seed): 0.932 RNASLOpt: 0.521 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 RNAfold: 0.477 Sensitivity CentroidAlifold(seed): 0.615 RNAfold: 0.471 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 HotKnots: 0.603 Sensitivity CentroidAlifold(seed): 0.634 HotKnots: 0.588 Positive Predictive Value CentroidAlifold(seed): 0.933 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RDfolder: 0.616 Sensitivity CentroidAlifold(seed): 0.642 RDfolder: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.936 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.723 CMfinder(20): 0.504 Sensitivity CentroidAlifold(seed): 0.550 CMfinder(20): 0.331 Positive Predictive Value CentroidAlifold(seed): 0.952 CMfinder(20): 0.771 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 RNAshapes: 0.486 Sensitivity CentroidAlifold(seed): 0.528 RNAshapes: 0.470 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAshapes: 0.506 Number of pairs reference - predicted secondary structure: 270 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 CRWrnafold: 0.476 Sensitivity CentroidAlifold(seed): 0.604 CRWrnafold: 0.468 Positive Predictive Value CentroidAlifold(seed): 0.914 CRWrnafold: 0.486 Number of pairs reference - predicted secondary structure: 323 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 Carnac(20): 0.512 Sensitivity CentroidAlifold(seed): 0.647 Carnac(20): 0.289 Positive Predictive Value CentroidAlifold(seed): 0.917 Carnac(20): 0.909 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.698 Vsfold5: 0.381 Sensitivity CentroidAlifold(seed): 0.529 Vsfold5: 0.351 Positive Predictive Value CentroidAlifold(seed): 0.922 Vsfold5: 0.416 Number of pairs reference - predicted secondary structure: 272 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.698 Vsfold4: 0.407 Sensitivity CentroidAlifold(seed): 0.529 Vsfold4: 0.367 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold4: 0.454 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 RNAwolf: 0.373 Sensitivity CentroidAlifold(seed): 0.522 RNAwolf: 0.382 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 294 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.473 CMfinder(seed): 0.363 Sensitivity CentroidAlifold(seed): 0.295 CMfinder(seed): 0.184 Positive Predictive Value CentroidAlifold(seed): 0.759 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.680 Carnac(seed): 0.253 Sensitivity CentroidAlifold(seed): 0.514 Carnac(seed): 0.068 Positive Predictive Value CentroidAlifold(seed): 0.899 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 RSpredict(20): 0.500 Sensitivity CentroidAlifold(seed): 0.647 RSpredict(20): 0.393 Positive Predictive Value CentroidAlifold(seed): 0.917 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Alterna: 0.486 Sensitivity CentroidAlifold(seed): 0.642 Alterna: 0.455 Positive Predictive Value CentroidAlifold(seed): 0.936 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 NanoFolder: 0.184 Sensitivity CentroidAlifold(seed): 0.514 NanoFolder: 0.210 Positive Predictive Value CentroidAlifold(seed): 0.913 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 RSpredict(seed): 0.364 Sensitivity CentroidAlifold(seed): 0.610 RSpredict(seed): 0.223 Positive Predictive Value CentroidAlifold(seed): 0.908 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 351 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.689 Mastr(20): 0.050 Sensitivity CentroidAlifold(seed): 0.517 Mastr(20): 0.003 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Mastr(seed): 0.041 Sensitivity CentroidAlifold(seed): 0.513 Mastr(seed): 0.003 Positive Predictive Value CentroidAlifold(seed): 0.910 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 270 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Multilign(seed): 0.575 Sensitivity CentroidAlifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 PPfold(seed): 0.666 Sensitivity CentroidAlifold(seed): 0.536 PPfold(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 MCFold: 0.358 Sensitivity CentroidAlifold(seed): 0.642 MCFold: 0.409 Positive Predictive Value CentroidAlifold(seed): 0.944 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08
CentroidHomfold‑LAST	523 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 CentroidHomfold‑LAST: 0.651 Sensitivity PETfold_pre2.0(seed): 0.592 CentroidHomfold‑LAST: 0.483 Positive Predictive Value PETfold_pre2.0(seed): 0.788 CentroidHomfold‑LAST: 0.879 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.726 CentroidHomfold‑LAST: 0.638 Sensitivity ContextFold: 0.683 CentroidHomfold‑LAST: 0.468 Positive Predictive Value ContextFold: 0.773 CentroidHomfold‑LAST: 0.870 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	290 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 CentroidHomfold‑LAST: 0.675 Sensitivity CentroidAlifold(seed): 0.524 CentroidHomfold‑LAST: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.920 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 290 Wilcoxon single-rank test P-value: 3.56938820447e-08		- TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidHomfold‑LAST: 0.703 Sensitivity TurboFold(20): 0.685 CentroidHomfold‑LAST: 0.552 Positive Predictive Value TurboFold(20): 0.802 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidHomfold‑LAST: 0.703 Sensitivity PETfold_pre2.0(20): 0.653 CentroidHomfold‑LAST: 0.552 Positive Predictive Value PETfold_pre2.0(20): 0.830 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.735 CentroidHomfold‑LAST: 0.703 Sensitivity PPfold(20): 0.635 CentroidHomfold‑LAST: 0.551 Positive Predictive Value PPfold(20): 0.851 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Cylofold: 0.701 CentroidHomfold‑LAST: 0.562 Sensitivity Cylofold: 0.673 CentroidHomfold‑LAST: 0.489 Positive Predictive Value Cylofold: 0.734 CentroidHomfold‑LAST: 0.652 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.718 CentroidHomfold‑LAST: 0.703 Sensitivity CentroidAlifold(20): 0.562 CentroidHomfold‑LAST: 0.552 Positive Predictive Value CentroidAlifold(20): 0.917 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 IPknot: 0.603 Sensitivity CentroidHomfold‑LAST: 0.468 IPknot: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.870 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: 0.697 CentroidHomfold‑LAST: 0.541 Sensitivity Pknots: 0.668 CentroidHomfold‑LAST: 0.471 Positive Predictive Value Pknots: 0.733 CentroidHomfold‑LAST: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 MXScarna(seed): 0.598 Sensitivity CentroidHomfold‑LAST: 0.509 MXScarna(seed): 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 RNAalifold(20): 0.661 Sensitivity CentroidHomfold‑LAST: 0.552 RNAalifold(20): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 CentroidFold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.468 CentroidFold: 0.518 Positive Predictive Value CentroidHomfold‑LAST: 0.870 CentroidFold: 0.636 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidHomfold‑LAST: 0.583 Sensitivity RNASampler(seed): 0.572 CentroidHomfold‑LAST: 0.502 Positive Predictive Value RNASampler(seed): 0.755 CentroidHomfold‑LAST: 0.684 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.1398907247e-09	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.701 Multilign(20): 0.651 Sensitivity CentroidHomfold‑LAST: 0.549 Multilign(20): 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.895 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 RNAalifold(seed): 0.473 Sensitivity CentroidHomfold‑LAST: 0.508 RNAalifold(seed): 0.276 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 291 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.682 RNASampler(20): 0.553 Sensitivity CentroidHomfold‑LAST: 0.537 RNASampler(20): 0.434 Positive Predictive Value CentroidHomfold‑LAST: 0.865 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 MXScarna(20): 0.627 Sensitivity CentroidHomfold‑LAST: 0.552 MXScarna(20): 0.553 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(20): 0.713 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Contrafold: 0.555 Sensitivity CentroidHomfold‑LAST: 0.468 Contrafold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Contrafold: 0.571 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Murlet(20): 0.550 Sensitivity CentroidHomfold‑LAST: 0.547 Murlet(20): 0.416 Positive Predictive Value CentroidHomfold‑LAST: 0.888 Murlet(20): 0.727 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Sfold: 0.516 Sensitivity CentroidHomfold‑LAST: 0.468 Sfold: 0.465 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Sfold: 0.574 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 ProbKnot: 0.524 Sensitivity CentroidHomfold‑LAST: 0.468 ProbKnot: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.870 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 MaxExpect: 0.525 Sensitivity CentroidHomfold‑LAST: 0.468 MaxExpect: 0.511 Positive Predictive Value CentroidHomfold‑LAST: 0.870 MaxExpect: 0.541 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 McQFold: 0.459 Sensitivity CentroidHomfold‑LAST: 0.468 McQFold: 0.449 Positive Predictive Value CentroidHomfold‑LAST: 0.870 McQFold: 0.472 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Murlet(seed): 0.482 Sensitivity CentroidHomfold‑LAST: 0.502 Murlet(seed): 0.319 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Fold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.468 Fold: 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Fold: 0.499 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 PknotsRG: 0.479 Sensitivity CentroidHomfold‑LAST: 0.468 PknotsRG: 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.870 PknotsRG: 0.480 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 UNAFold: 0.478 Sensitivity CentroidHomfold‑LAST: 0.468 UNAFold: 0.474 Positive Predictive Value CentroidHomfold‑LAST: 0.870 UNAFold: 0.483 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.649 TurboFold(seed): 0.633 Sensitivity CentroidHomfold‑LAST: 0.562 TurboFold(seed): 0.562 Positive Predictive Value CentroidHomfold‑LAST: 0.753 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.45329040827e-07	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAsubopt: 0.473 Sensitivity CentroidHomfold‑LAST: 0.468 RNAsubopt: 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.651 Afold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.486 Afold: 0.493 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Afold: 0.508 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.643 RNASLOpt: 0.446 Sensitivity CentroidHomfold‑LAST: 0.479 RNASLOpt: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.865 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAfold: 0.478 Sensitivity CentroidHomfold‑LAST: 0.468 RNAfold: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAfold: 0.479 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 HotKnots: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 HotKnots: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.592 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 RDfolder: 0.508 Sensitivity CentroidHomfold‑LAST: 0.471 RDfolder: 0.432 Positive Predictive Value CentroidHomfold‑LAST: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 8.1815824276e-08	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 CMfinder(20): 0.482 Sensitivity CentroidHomfold‑LAST: 0.552 CMfinder(20): 0.310 Positive Predictive Value CentroidHomfold‑LAST: 0.896 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAshapes: 0.408 Sensitivity CentroidHomfold‑LAST: 0.474 RNAshapes: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.868 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 CRWrnafold: 0.422 Sensitivity CentroidHomfold‑LAST: 0.468 CRWrnafold: 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.870 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Carnac(20): 0.365 Sensitivity CentroidHomfold‑LAST: 0.552 Carnac(20): 0.155 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Vsfold5: 0.333 Sensitivity CentroidHomfold‑LAST: 0.473 Vsfold5: 0.317 Positive Predictive Value CentroidHomfold‑LAST: 0.869 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Vsfold4: 0.337 Sensitivity CentroidHomfold‑LAST: 0.474 Vsfold4: 0.310 Positive Predictive Value CentroidHomfold‑LAST: 0.869 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAwolf: 0.339 Sensitivity CentroidHomfold‑LAST: 0.468 RNAwolf: 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAwolf: 0.327 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.651 CMfinder(seed): 0.363 Sensitivity CentroidHomfold‑LAST: 0.493 CMfinder(seed): 0.184 Positive Predictive Value CentroidHomfold‑LAST: 0.860 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.632 Carnac(seed): 0.146 Sensitivity CentroidHomfold‑LAST: 0.466 Carnac(seed): 0.022 Positive Predictive Value CentroidHomfold‑LAST: 0.858 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 RSpredict(20): 0.350 Sensitivity CentroidHomfold‑LAST: 0.552 RSpredict(20): 0.222 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 Alterna: 0.393 Sensitivity CentroidHomfold‑LAST: 0.471 Alterna: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 NanoFolder: 0.176 Sensitivity CentroidHomfold‑LAST: 0.480 NanoFolder: 0.209 Positive Predictive Value CentroidHomfold‑LAST: 0.876 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RSpredict(seed): 0.065 Sensitivity CentroidHomfold‑LAST: 0.509 RSpredict(seed): 0.017 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(seed): 0.254 Number of pairs reference - predicted secondary structure: 293 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Mastr(20): 0.044 Sensitivity CentroidHomfold‑LAST: 0.552 Mastr(20): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Mastr(seed): 0.042 Sensitivity CentroidHomfold‑LAST: 0.511 Mastr(seed): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Multilign(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.486 Multilign(seed): 0.536 Positive Predictive Value CentroidHomfold‑LAST: 0.708 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidHomfold‑LAST: 0.584 Sensitivity PPfold(seed): 0.536 CentroidHomfold‑LAST: 0.486 Positive Predictive Value PPfold(seed): 0.833 CentroidHomfold‑LAST: 0.708 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.487 MCFold: 0.290 Sensitivity CentroidHomfold‑LAST: 0.422 MCFold: 0.320 Positive Predictive Value CentroidHomfold‑LAST: 0.570 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(20)	209 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 TurboFold(20): 0.741 Sensitivity PETfold_pre2.0(seed): 0.674 TurboFold(20): 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.845 TurboFold(20): 0.802 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.840 TurboFold(20): 0.741 Sensitivity ContextFold: 0.791 TurboFold(20): 0.685 Positive Predictive Value ContextFold: 0.892 TurboFold(20): 0.802 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	166 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 CentroidAlifold(seed): 0.723 Sensitivity TurboFold(20): 0.703 CentroidAlifold(seed): 0.550 Positive Predictive Value TurboFold(20): 0.824 CentroidAlifold(seed): 0.952 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidHomfold‑LAST: 0.703 Sensitivity TurboFold(20): 0.685 CentroidHomfold‑LAST: 0.552 Positive Predictive Value TurboFold(20): 0.802 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.741 PETfold_pre2.0(20): 0.735 Sensitivity TurboFold(20): 0.685 PETfold_pre2.0(20): 0.653 Positive Predictive Value TurboFold(20): 0.802 PETfold_pre2.0(20): 0.830 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 PPfold(20): 0.735 Sensitivity TurboFold(20): 0.684 PPfold(20): 0.635 Positive Predictive Value TurboFold(20): 0.801 PPfold(20): 0.851 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 9.49173053431e-08	? TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.857 Cylofold: 0.756 Sensitivity TurboFold(20): 0.744 Cylofold: 0.677 Positive Predictive Value TurboFold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidAlifold(20): 0.718 Sensitivity TurboFold(20): 0.685 CentroidAlifold(20): 0.562 Positive Predictive Value TurboFold(20): 0.802 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.741 IPknot: 0.649 Sensitivity TurboFold(20): 0.685 IPknot: 0.575 Positive Predictive Value TurboFold(20): 0.802 IPknot: 0.734 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.857 Pknots: 0.723 Sensitivity TurboFold(20): 0.744 Pknots: 0.632 Positive Predictive Value TurboFold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 MXScarna(seed): 0.656 Sensitivity TurboFold(20): 0.703 MXScarna(seed): 0.543 Positive Predictive Value TurboFold(20): 0.823 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.741 RNAalifold(20): 0.661 Sensitivity TurboFold(20): 0.685 RNAalifold(20): 0.533 Positive Predictive Value TurboFold(20): 0.802 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidFold: 0.617 Sensitivity TurboFold(20): 0.685 CentroidFold: 0.548 Positive Predictive Value TurboFold(20): 0.802 CentroidFold: 0.696 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Multilign(20): 0.651 Sensitivity TurboFold(20): 0.684 Multilign(20): 0.591 Positive Predictive Value TurboFold(20): 0.801 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RNAalifold(seed): 0.448 Sensitivity TurboFold(20): 0.703 RNAalifold(seed): 0.252 Positive Predictive Value TurboFold(20): 0.824 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.668 RNASampler(20): 0.553 Sensitivity TurboFold(20): 0.614 RNASampler(20): 0.434 Positive Predictive Value TurboFold(20): 0.727 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.741 MXScarna(20): 0.627 Sensitivity TurboFold(20): 0.685 MXScarna(20): 0.553 Positive Predictive Value TurboFold(20): 0.802 MXScarna(20): 0.713 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.741 Contrafold: 0.602 Sensitivity TurboFold(20): 0.685 Contrafold: 0.577 Positive Predictive Value TurboFold(20): 0.802 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.730 Murlet(20): 0.550 Sensitivity TurboFold(20): 0.675 Murlet(20): 0.416 Positive Predictive Value TurboFold(20): 0.791 Murlet(20): 0.727 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.741 Sfold: 0.569 Sensitivity TurboFold(20): 0.685 Sfold: 0.503 Positive Predictive Value TurboFold(20): 0.802 Sfold: 0.644 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.741 ProbKnot: 0.587 Sensitivity TurboFold(20): 0.685 ProbKnot: 0.565 Positive Predictive Value TurboFold(20): 0.802 ProbKnot: 0.611 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.741 MaxExpect: 0.588 Sensitivity TurboFold(20): 0.685 MaxExpect: 0.562 Positive Predictive Value TurboFold(20): 0.802 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.741 McQFold: 0.454 Sensitivity TurboFold(20): 0.685 McQFold: 0.434 Positive Predictive Value TurboFold(20): 0.802 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): N/A Murlet(seed): N/A Sensitivity TurboFold(20): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.741 Fold: 0.551 Sensitivity TurboFold(20): 0.685 Fold: 0.542 Positive Predictive Value TurboFold(20): 0.802 Fold: 0.562 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.741 PknotsRG: 0.513 Sensitivity TurboFold(20): 0.685 PknotsRG: 0.504 Positive Predictive Value TurboFold(20): 0.802 PknotsRG: 0.524 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.741 UNAFold: 0.532 Sensitivity TurboFold(20): 0.685 UNAFold: 0.520 Positive Predictive Value TurboFold(20): 0.802 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs TurboFold(20) Matthews Correlation Coefficient TurboFold(seed): N/A TurboFold(20): N/A Sensitivity TurboFold(seed): N/A TurboFold(20): N/A Positive Predictive Value TurboFold(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.741 RNAsubopt: 0.520 Sensitivity TurboFold(20): 0.685 RNAsubopt: 0.518 Positive Predictive Value TurboFold(20): 0.802 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.756 Afold: 0.548 Sensitivity TurboFold(20): 0.699 Afold: 0.533 Positive Predictive Value TurboFold(20): 0.819 Afold: 0.565 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.736 RNASLOpt: 0.456 Sensitivity TurboFold(20): 0.681 RNASLOpt: 0.421 Positive Predictive Value TurboFold(20): 0.797 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.741 RNAfold: 0.528 Sensitivity TurboFold(20): 0.685 RNAfold: 0.519 Positive Predictive Value TurboFold(20): 0.802 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.857 HotKnots: 0.717 Sensitivity TurboFold(20): 0.744 HotKnots: 0.639 Positive Predictive Value TurboFold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.857 RDfolder: 0.664 Sensitivity TurboFold(20): 0.744 RDfolder: 0.586 Positive Predictive Value TurboFold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.741 CMfinder(20): 0.482 Sensitivity TurboFold(20): 0.685 CMfinder(20): 0.310 Positive Predictive Value TurboFold(20): 0.802 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.739 RNAshapes: 0.457 Sensitivity TurboFold(20): 0.683 RNAshapes: 0.442 Positive Predictive Value TurboFold(20): 0.800 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.741 CRWrnafold: 0.456 Sensitivity TurboFold(20): 0.685 CRWrnafold: 0.447 Positive Predictive Value TurboFold(20): 0.802 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.741 Carnac(20): 0.365 Sensitivity TurboFold(20): 0.685 Carnac(20): 0.155 Positive Predictive Value TurboFold(20): 0.802 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold5: 0.371 Sensitivity TurboFold(20): 0.683 Vsfold5: 0.344 Positive Predictive Value TurboFold(20): 0.800 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.739 Vsfold4: 0.392 Sensitivity TurboFold(20): 0.684 Vsfold4: 0.355 Positive Predictive Value TurboFold(20): 0.800 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.741 RNAwolf: 0.368 Sensitivity TurboFold(20): 0.685 RNAwolf: 0.378 Positive Predictive Value TurboFold(20): 0.802 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-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 Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.781 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.777 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.786 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.741 RSpredict(20): 0.350 Sensitivity TurboFold(20): 0.685 RSpredict(20): 0.222 Positive Predictive Value TurboFold(20): 0.802 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.857 Alterna: 0.656 Sensitivity TurboFold(20): 0.744 Alterna: 0.602 Positive Predictive Value TurboFold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.729 NanoFolder: 0.152 Sensitivity TurboFold(20): 0.674 NanoFolder: 0.174 Positive Predictive Value TurboFold(20): 0.789 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RSpredict(seed): 0.063 Sensitivity TurboFold(20): 0.703 RSpredict(seed): 0.016 Positive Predictive Value TurboFold(20): 0.824 RSpredict(seed): 0.246 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.741 Mastr(20): 0.044 Sensitivity TurboFold(20): 0.685 Mastr(20): 0.003 Positive Predictive Value TurboFold(20): 0.802 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.761 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.823 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): N/A PPfold(seed): N/A Sensitivity TurboFold(20): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.857 MCFold: 0.291 Sensitivity TurboFold(20): 0.744 MCFold: 0.323 Positive Predictive Value TurboFold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(20)	286 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 PETfold_pre2.0(20): 0.730 Sensitivity PETfold_pre2.0(seed): 0.709 PETfold_pre2.0(20): 0.681 Positive Predictive Value PETfold_pre2.0(seed): 0.810 PETfold_pre2.0(20): 0.783 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.767 PETfold_pre2.0(20): 0.730 Sensitivity ContextFold: 0.726 PETfold_pre2.0(20): 0.681 Positive Predictive Value ContextFold: 0.811 PETfold_pre2.0(20): 0.783 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.774 CentroidAlifold(seed): 0.770 Sensitivity PETfold_pre2.0(20): 0.725 CentroidAlifold(seed): 0.647 Positive Predictive Value PETfold_pre2.0(20): 0.827 CentroidAlifold(seed): 0.917 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidHomfold‑LAST: 0.703 Sensitivity PETfold_pre2.0(20): 0.653 CentroidHomfold‑LAST: 0.552 Positive Predictive Value PETfold_pre2.0(20): 0.830 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.741 PETfold_pre2.0(20): 0.735 Sensitivity TurboFold(20): 0.685 PETfold_pre2.0(20): 0.653 Positive Predictive Value TurboFold(20): 0.802 PETfold_pre2.0(20): 0.830 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 PPfold(20): 0.736 Sensitivity PETfold_pre2.0(20): 0.660 PPfold(20): 0.641 Positive Predictive Value PETfold_pre2.0(20): 0.823 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 6.06606238843e-08	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Cylofold: 0.756 Sensitivity PETfold_pre2.0(20): 0.759 Cylofold: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 CentroidAlifold(20): 0.723 Sensitivity PETfold_pre2.0(20): 0.681 CentroidAlifold(20): 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.783 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 IPknot: 0.577 Sensitivity PETfold_pre2.0(20): 0.681 IPknot: 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.783 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Pknots: 0.723 Sensitivity PETfold_pre2.0(20): 0.759 Pknots: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.962 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.774 MXScarna(seed): 0.661 Sensitivity PETfold_pre2.0(20): 0.724 MXScarna(seed): 0.575 Positive Predictive Value PETfold_pre2.0(20): 0.827 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RNAalifold(20): 0.668 Sensitivity PETfold_pre2.0(20): 0.681 RNAalifold(20): 0.588 Positive Predictive Value PETfold_pre2.0(20): 0.783 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.731 CentroidFold: 0.539 Sensitivity PETfold_pre2.0(20): 0.682 CentroidFold: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.785 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Multilign(20): 0.651 Sensitivity PETfold_pre2.0(20): 0.653 Multilign(20): 0.591 Positive Predictive Value PETfold_pre2.0(20): 0.830 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.765 RNAalifold(seed): 0.650 Sensitivity PETfold_pre2.0(20): 0.716 RNAalifold(seed): 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.817 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.656 RNASampler(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.575 RNASampler(20): 0.434 Positive Predictive Value PETfold_pre2.0(20): 0.749 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 MXScarna(20): 0.608 Sensitivity PETfold_pre2.0(20): 0.681 MXScarna(20): 0.550 Positive Predictive Value PETfold_pre2.0(20): 0.783 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Contrafold: 0.523 Sensitivity PETfold_pre2.0(20): 0.681 Contrafold: 0.504 Positive Predictive Value PETfold_pre2.0(20): 0.783 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.727 Murlet(20): 0.566 Sensitivity PETfold_pre2.0(20): 0.656 Murlet(20): 0.445 Positive Predictive Value PETfold_pre2.0(20): 0.805 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Sfold: 0.496 Sensitivity PETfold_pre2.0(20): 0.681 Sfold: 0.440 Positive Predictive Value PETfold_pre2.0(20): 0.783 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 ProbKnot: 0.473 Sensitivity PETfold_pre2.0(20): 0.681 ProbKnot: 0.463 Positive Predictive Value PETfold_pre2.0(20): 0.783 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 MaxExpect: 0.478 Sensitivity PETfold_pre2.0(20): 0.681 MaxExpect: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.783 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 McQFold: 0.454 Sensitivity PETfold_pre2.0(20): 0.653 McQFold: 0.434 Positive Predictive Value PETfold_pre2.0(20): 0.830 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Murlet(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Murlet(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Fold: 0.445 Sensitivity PETfold_pre2.0(20): 0.681 Fold: 0.446 Positive Predictive Value PETfold_pre2.0(20): 0.783 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.785 PknotsRG: 0.482 Sensitivity PETfold_pre2.0(20): 0.732 PknotsRG: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.841 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 UNAFold: 0.459 Sensitivity PETfold_pre2.0(20): 0.681 UNAFold: 0.454 Positive Predictive Value PETfold_pre2.0(20): 0.783 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAsubopt: 0.520 Sensitivity PETfold_pre2.0(20): 0.653 RNAsubopt: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.830 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.734 Afold: 0.453 Sensitivity PETfold_pre2.0(20): 0.687 Afold: 0.449 Positive Predictive Value PETfold_pre2.0(20): 0.785 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 RNASLOpt: 0.456 Sensitivity PETfold_pre2.0(20): 0.658 RNASLOpt: 0.421 Positive Predictive Value PETfold_pre2.0(20): 0.828 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RNAfold: 0.444 Sensitivity PETfold_pre2.0(20): 0.681 RNAfold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.783 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 HotKnots: 0.717 Sensitivity PETfold_pre2.0(20): 0.759 HotKnots: 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.962 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RDfolder: 0.664 Sensitivity PETfold_pre2.0(20): 0.759 RDfolder: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.962 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(20): 0.653 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(20): 0.830 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.738 RNAshapes: 0.457 Sensitivity PETfold_pre2.0(20): 0.655 RNAshapes: 0.442 Positive Predictive Value PETfold_pre2.0(20): 0.831 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.771 CRWrnafold: 0.484 Sensitivity PETfold_pre2.0(20): 0.710 CRWrnafold: 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.837 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Carnac(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.681 Carnac(20): 0.277 Positive Predictive Value PETfold_pre2.0(20): 0.783 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Vsfold5: 0.371 Sensitivity PETfold_pre2.0(20): 0.656 Vsfold5: 0.344 Positive Predictive Value PETfold_pre2.0(20): 0.830 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Vsfold4: 0.392 Sensitivity PETfold_pre2.0(20): 0.655 Vsfold4: 0.355 Positive Predictive Value PETfold_pre2.0(20): 0.830 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAwolf: 0.368 Sensitivity PETfold_pre2.0(20): 0.653 RNAwolf: 0.378 Positive Predictive Value PETfold_pre2.0(20): 0.830 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-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 Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.860 Carnac(seed): 0.552 Sensitivity PETfold_pre2.0(20): 0.830 Carnac(seed): 0.327 Positive Predictive Value PETfold_pre2.0(20): 0.891 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RSpredict(20): 0.425 Sensitivity PETfold_pre2.0(20): 0.681 RSpredict(20): 0.345 Positive Predictive Value PETfold_pre2.0(20): 0.783 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Alterna: 0.656 Sensitivity PETfold_pre2.0(20): 0.759 Alterna: 0.602 Positive Predictive Value PETfold_pre2.0(20): 0.962 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 NanoFolder: 0.152 Sensitivity PETfold_pre2.0(20): 0.650 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.831 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.771 RSpredict(seed): 0.402 Sensitivity PETfold_pre2.0(20): 0.719 RSpredict(seed): 0.269 Positive Predictive Value PETfold_pre2.0(20): 0.826 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.670 Mastr(20): 0.035 Sensitivity PETfold_pre2.0(20): 0.607 Mastr(20): 0.002 Positive Predictive Value PETfold_pre2.0(20): 0.739 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.668 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MCFold: 0.291 Sensitivity PETfold_pre2.0(20): 0.759 MCFold: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.962 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	208 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 PPfold(20): 0.736 Sensitivity PETfold_pre2.0(seed): 0.682 PPfold(20): 0.641 Positive Predictive Value PETfold_pre2.0(seed): 0.840 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.829 PPfold(20): 0.736 Sensitivity ContextFold: 0.780 PPfold(20): 0.641 Positive Predictive Value ContextFold: 0.881 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.760 CentroidAlifold(seed): 0.737 Sensitivity PPfold(20): 0.668 CentroidAlifold(seed): 0.573 Positive Predictive Value PPfold(20): 0.864 CentroidAlifold(seed): 0.948 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.735 CentroidHomfold‑LAST: 0.703 Sensitivity PPfold(20): 0.635 CentroidHomfold‑LAST: 0.551 Positive Predictive Value PPfold(20): 0.851 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 PPfold(20): 0.735 Sensitivity TurboFold(20): 0.684 PPfold(20): 0.635 Positive Predictive Value TurboFold(20): 0.801 PPfold(20): 0.851 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 9.49173053431e-08	208 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 PPfold(20): 0.736 Sensitivity PETfold_pre2.0(20): 0.660 PPfold(20): 0.641 Positive Predictive Value PETfold_pre2.0(20): 0.823 PPfold(20): 0.846 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 6.06606238843e-08		? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.840 Cylofold: 0.756 Sensitivity PPfold(20): 0.737 Cylofold: 0.677 Positive Predictive Value PPfold(20): 0.961 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.736 CentroidAlifold(20): 0.721 Sensitivity PPfold(20): 0.641 CentroidAlifold(20): 0.571 Positive Predictive Value PPfold(20): 0.846 CentroidAlifold(20): 0.911 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.736 IPknot: 0.638 Sensitivity PPfold(20): 0.641 IPknot: 0.562 Positive Predictive Value PPfold(20): 0.846 IPknot: 0.725 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.840 Pknots: 0.723 Sensitivity PPfold(20): 0.737 Pknots: 0.632 Positive Predictive Value PPfold(20): 0.961 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.760 MXScarna(seed): 0.665 Sensitivity PPfold(20): 0.668 MXScarna(seed): 0.553 Positive Predictive Value PPfold(20): 0.865 MXScarna(seed): 0.799 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.736 RNAalifold(20): 0.664 Sensitivity PPfold(20): 0.641 RNAalifold(20): 0.545 Positive Predictive Value PPfold(20): 0.846 RNAalifold(20): 0.808 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.736 CentroidFold: 0.601 Sensitivity PPfold(20): 0.641 CentroidFold: 0.531 Positive Predictive Value PPfold(20): 0.846 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.735 Multilign(20): 0.652 Sensitivity PPfold(20): 0.635 Multilign(20): 0.591 Positive Predictive Value PPfold(20): 0.852 Multilign(20): 0.719 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.751 RNAalifold(seed): 0.494 Sensitivity PPfold(20): 0.661 RNAalifold(seed): 0.307 Positive Predictive Value PPfold(20): 0.855 RNAalifold(seed): 0.796 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.661 RNASampler(20): 0.553 Sensitivity PPfold(20): 0.547 RNASampler(20): 0.434 Positive Predictive Value PPfold(20): 0.800 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.736 MXScarna(20): 0.628 Sensitivity PPfold(20): 0.641 MXScarna(20): 0.556 Positive Predictive Value PPfold(20): 0.846 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.736 Contrafold: 0.586 Sensitivity PPfold(20): 0.641 Contrafold: 0.561 Positive Predictive Value PPfold(20): 0.846 Contrafold: 0.612 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.726 Murlet(20): 0.554 Sensitivity PPfold(20): 0.627 Murlet(20): 0.420 Positive Predictive Value PPfold(20): 0.842 Murlet(20): 0.731 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.736 Sfold: 0.558 Sensitivity PPfold(20): 0.641 Sfold: 0.489 Positive Predictive Value PPfold(20): 0.846 Sfold: 0.637 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.736 ProbKnot: 0.563 Sensitivity PPfold(20): 0.641 ProbKnot: 0.543 Positive Predictive Value PPfold(20): 0.846 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.736 MaxExpect: 0.564 Sensitivity PPfold(20): 0.641 MaxExpect: 0.540 Positive Predictive Value PPfold(20): 0.846 MaxExpect: 0.591 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.735 McQFold: 0.454 Sensitivity PPfold(20): 0.635 McQFold: 0.434 Positive Predictive Value PPfold(20): 0.851 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): N/A Murlet(seed): N/A Sensitivity PPfold(20): N/A Murlet(seed): N/A Positive Predictive Value PPfold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.736 Fold: 0.529 Sensitivity PPfold(20): 0.641 Fold: 0.521 Positive Predictive Value PPfold(20): 0.846 Fold: 0.538 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.742 PknotsRG: 0.506 Sensitivity PPfold(20): 0.646 PknotsRG: 0.496 Positive Predictive Value PPfold(20): 0.854 PknotsRG: 0.517 Number of pairs reference - predicted secondary structure: 206 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.736 UNAFold: 0.520 Sensitivity PPfold(20): 0.641 UNAFold: 0.508 Positive Predictive Value PPfold(20): 0.846 UNAFold: 0.534 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(20): N/A Sensitivity TurboFold(seed): N/A PPfold(20): N/A Positive Predictive Value TurboFold(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.735 RNAsubopt: 0.520 Sensitivity PPfold(20): 0.635 RNAsubopt: 0.518 Positive Predictive Value PPfold(20): 0.851 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.744 Afold: 0.529 Sensitivity PPfold(20): 0.650 Afold: 0.514 Positive Predictive Value PPfold(20): 0.852 Afold: 0.544 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.738 RNASLOpt: 0.457 Sensitivity PPfold(20): 0.640 RNASLOpt: 0.421 Positive Predictive Value PPfold(20): 0.851 RNASLOpt: 0.497 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.736 RNAfold: 0.515 Sensitivity PPfold(20): 0.641 RNAfold: 0.507 Positive Predictive Value PPfold(20): 0.846 RNAfold: 0.525 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.840 HotKnots: 0.717 Sensitivity PPfold(20): 0.737 HotKnots: 0.639 Positive Predictive Value PPfold(20): 0.961 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.840 RDfolder: 0.664 Sensitivity PPfold(20): 0.737 RDfolder: 0.586 Positive Predictive Value PPfold(20): 0.961 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.735 CMfinder(20): 0.482 Sensitivity PPfold(20): 0.635 CMfinder(20): 0.311 Positive Predictive Value PPfold(20): 0.851 CMfinder(20): 0.750 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.738 RNAshapes: 0.456 Sensitivity PPfold(20): 0.639 RNAshapes: 0.441 Positive Predictive Value PPfold(20): 0.854 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 193 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.740 CRWrnafold: 0.464 Sensitivity PPfold(20): 0.643 CRWrnafold: 0.455 Positive Predictive Value PPfold(20): 0.852 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.736 Carnac(20): 0.398 Sensitivity PPfold(20): 0.641 Carnac(20): 0.181 Positive Predictive Value PPfold(20): 0.846 Carnac(20): 0.878 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.738 Vsfold5: 0.370 Sensitivity PPfold(20): 0.639 Vsfold5: 0.343 Positive Predictive Value PPfold(20): 0.852 Vsfold5: 0.402 Number of pairs reference - predicted secondary structure: 195 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.737 Vsfold4: 0.392 Sensitivity PPfold(20): 0.638 Vsfold4: 0.355 Positive Predictive Value PPfold(20): 0.852 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.735 RNAwolf: 0.370 Sensitivity PPfold(20): 0.635 RNAwolf: 0.380 Positive Predictive Value PPfold(20): 0.851 RNAwolf: 0.362 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-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 Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.818 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.738 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.907 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.736 RSpredict(20): 0.374 Sensitivity PPfold(20): 0.641 RSpredict(20): 0.252 Positive Predictive Value PPfold(20): 0.846 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.840 Alterna: 0.656 Sensitivity PPfold(20): 0.737 Alterna: 0.602 Positive Predictive Value PPfold(20): 0.961 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.734 NanoFolder: 0.155 Sensitivity PPfold(20): 0.633 NanoFolder: 0.178 Positive Predictive Value PPfold(20): 0.850 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.760 RSpredict(seed): 0.191 Sensitivity PPfold(20): 0.669 RSpredict(seed): 0.070 Positive Predictive Value PPfold(20): 0.865 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.728 Mastr(20): 0.044 Sensitivity PPfold(20): 0.630 Mastr(20): 0.003 Positive Predictive Value PPfold(20): 0.843 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.755 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.661 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.864 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): N/A PPfold(seed): N/A Sensitivity PPfold(20): N/A PPfold(seed): N/A Positive Predictive Value PPfold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.840 MCFold: 0.291 Sensitivity PPfold(20): 0.737 MCFold: 0.323 Positive Predictive Value PPfold(20): 0.961 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Cylofold	17 Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.809 PETfold_pre2.0(seed): 0.737 Sensitivity Cylofold: 0.782 PETfold_pre2.0(seed): 0.666 Positive Predictive Value Cylofold: 0.841 PETfold_pre2.0(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	47 Cylofold vs ContextFold Matthews Correlation Coefficient Cylofold: 0.701 ContextFold: 0.566 Sensitivity Cylofold: 0.673 ContextFold: 0.505 Positive Predictive Value Cylofold: 0.734 ContextFold: 0.640 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 CentroidAlifold(seed): 0.780 Sensitivity Cylofold: 0.772 CentroidAlifold(seed): 0.646 Positive Predictive Value Cylofold: 0.828 CentroidAlifold(seed): 0.946 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.17043147862e-08	47 Cylofold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Cylofold: 0.701 CentroidHomfold‑LAST: 0.562 Sensitivity Cylofold: 0.673 CentroidHomfold‑LAST: 0.489 Positive Predictive Value Cylofold: 0.734 CentroidHomfold‑LAST: 0.652 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.857 Cylofold: 0.756 Sensitivity TurboFold(20): 0.744 Cylofold: 0.677 Positive Predictive Value TurboFold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Cylofold: 0.756 Sensitivity PETfold_pre2.0(20): 0.759 Cylofold: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.840 Cylofold: 0.756 Sensitivity PPfold(20): 0.737 Cylofold: 0.677 Positive Predictive Value PPfold(20): 0.961 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Cylofold: 0.756 Sensitivity CentroidAlifold(20): 0.752 Cylofold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs IPknot Matthews Correlation Coefficient Cylofold: 0.701 IPknot: 0.569 Sensitivity Cylofold: 0.673 IPknot: 0.511 Positive Predictive Value Cylofold: 0.734 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.764 Pknots: 0.691 Sensitivity Cylofold: 0.742 Pknots: 0.662 Positive Predictive Value Cylofold: 0.791 Pknots: 0.728 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.798 MXScarna(seed): 0.542 Sensitivity Cylofold: 0.772 MXScarna(seed): 0.505 Positive Predictive Value Cylofold: 0.828 MXScarna(seed): 0.590 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	? RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.844 Cylofold: 0.756 Sensitivity RNAalifold(20): 0.722 Cylofold: 0.677 Positive Predictive Value RNAalifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs CentroidFold Matthews Correlation Coefficient Cylofold: 0.701 CentroidFold: 0.554 Sensitivity Cylofold: 0.673 CentroidFold: 0.497 Positive Predictive Value Cylofold: 0.734 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.831 RNASampler(seed): 0.646 Sensitivity Cylofold: 0.834 RNASampler(seed): 0.562 Positive Predictive Value Cylofold: 0.830 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09	? Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.862 Cylofold: 0.756 Sensitivity Multilign(20): 0.752 Cylofold: 0.677 Positive Predictive Value Multilign(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 RNAalifold(seed): 0.647 Sensitivity Cylofold: 0.772 RNAalifold(seed): 0.517 Positive Predictive Value Cylofold: 0.828 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.62913390836e-08	? RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.840 Cylofold: 0.756 Sensitivity RNASampler(20): 0.714 Cylofold: 0.677 Positive Predictive Value RNASampler(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.837 Cylofold: 0.756 Sensitivity MXScarna(20): 0.752 Cylofold: 0.677 Positive Predictive Value MXScarna(20): 0.935 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Contrafold Matthews Correlation Coefficient Cylofold: 0.701 Contrafold: 0.528 Sensitivity Cylofold: 0.673 Contrafold: 0.491 Positive Predictive Value Cylofold: 0.734 Contrafold: 0.575 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: 0.756 Murlet(20): 0.741 Sensitivity Cylofold: 0.677 Murlet(20): 0.594 Positive Predictive Value Cylofold: 0.849 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Sfold Matthews Correlation Coefficient Cylofold: 0.701 Sfold: 0.516 Sensitivity Cylofold: 0.673 Sfold: 0.460 Positive Predictive Value Cylofold: 0.734 Sfold: 0.585 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.701 ProbKnot: 0.541 Sensitivity Cylofold: 0.673 ProbKnot: 0.512 Positive Predictive Value Cylofold: 0.734 ProbKnot: 0.579 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.701 MaxExpect: 0.521 Sensitivity Cylofold: 0.673 MaxExpect: 0.483 Positive Predictive Value Cylofold: 0.734 MaxExpect: 0.570 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs McQFold Matthews Correlation Coefficient Cylofold: 0.701 McQFold: 0.676 Sensitivity Cylofold: 0.673 McQFold: 0.648 Positive Predictive Value Cylofold: 0.734 McQFold: 0.711 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 1.02208072244e-07	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.831 Murlet(seed): 0.405 Sensitivity Cylofold: 0.834 Murlet(seed): 0.263 Positive Predictive Value Cylofold: 0.830 Murlet(seed): 0.633 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.701 Fold: 0.528 Sensitivity Cylofold: 0.673 Fold: 0.491 Positive Predictive Value Cylofold: 0.734 Fold: 0.574 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.701 PknotsRG: 0.594 Sensitivity Cylofold: 0.673 PknotsRG: 0.572 Positive Predictive Value Cylofold: 0.734 PknotsRG: 0.623 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.701 UNAFold: 0.474 Sensitivity Cylofold: 0.673 UNAFold: 0.438 Positive Predictive Value Cylofold: 0.734 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.911 TurboFold(seed): 0.587 Sensitivity Cylofold: 0.914 TurboFold(seed): 0.513 Positive Predictive Value Cylofold: 0.908 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.701 RNAsubopt: 0.475 Sensitivity Cylofold: 0.673 RNAsubopt: 0.442 Positive Predictive Value Cylofold: 0.734 RNAsubopt: 0.518 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Afold Matthews Correlation Coefficient Cylofold: 0.653 Afold: 0.349 Sensitivity Cylofold: 0.630 Afold: 0.334 Positive Predictive Value Cylofold: 0.682 Afold: 0.372 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.701 RNASLOpt: 0.523 Sensitivity Cylofold: 0.673 RNASLOpt: 0.470 Positive Predictive Value Cylofold: 0.734 RNASLOpt: 0.590 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.701 RNAfold: 0.481 Sensitivity Cylofold: 0.673 RNAfold: 0.445 Positive Predictive Value Cylofold: 0.734 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: 0.764 HotKnots: 0.524 Sensitivity Cylofold: 0.742 HotKnots: 0.501 Positive Predictive Value Cylofold: 0.791 HotKnots: 0.560 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.764 RDfolder: 0.505 Sensitivity Cylofold: 0.742 RDfolder: 0.429 Positive Predictive Value Cylofold: 0.791 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.779 Cylofold: 0.756 Sensitivity CMfinder(20): 0.617 Cylofold: 0.677 Positive Predictive Value CMfinder(20): 0.988 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.701 RNAshapes: 0.471 Sensitivity Cylofold: 0.673 RNAshapes: 0.437 Positive Predictive Value Cylofold: 0.734 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.701 CRWrnafold: 0.469 Sensitivity Cylofold: 0.673 CRWrnafold: 0.430 Positive Predictive Value Cylofold: 0.734 CRWrnafold: 0.519 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.821 Cylofold: 0.756 Sensitivity Carnac(20): 0.684 Cylofold: 0.677 Positive Predictive Value Carnac(20): 0.989 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.701 Vsfold5: 0.557 Sensitivity Cylofold: 0.673 Vsfold5: 0.513 Positive Predictive Value Cylofold: 0.734 Vsfold5: 0.611 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.701 Vsfold4: 0.449 Sensitivity Cylofold: 0.673 Vsfold4: 0.395 Positive Predictive Value Cylofold: 0.734 Vsfold4: 0.517 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.701 RNAwolf: 0.389 Sensitivity Cylofold: 0.673 RNAwolf: 0.374 Positive Predictive Value Cylofold: 0.734 RNAwolf: 0.413 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: 0.797 CMfinder(seed): 0.439 Sensitivity Cylofold: 0.801 CMfinder(seed): 0.348 Positive Predictive Value Cylofold: 0.797 CMfinder(seed): 0.563 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.831 Carnac(seed): 0.550 Sensitivity Cylofold: 0.834 Carnac(seed): 0.313 Positive Predictive Value Cylofold: 0.830 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	? Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.756 RSpredict(20): 0.672 Sensitivity Cylofold: 0.677 RSpredict(20): 0.549 Positive Predictive Value Cylofold: 0.849 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.764 Alterna: 0.401 Sensitivity Cylofold: 0.742 Alterna: 0.372 Positive Predictive Value Cylofold: 0.791 Alterna: 0.446 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.663 NanoFolder: 0.191 Sensitivity Cylofold: 0.602 NanoFolder: 0.218 Positive Predictive Value Cylofold: 0.734 NanoFolder: 0.175 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.798 RSpredict(seed): 0.514 Sensitivity Cylofold: 0.772 RSpredict(seed): 0.434 Positive Predictive Value Cylofold: 0.828 RSpredict(seed): 0.618 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	? Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.756 Mastr(20): 0.561 Sensitivity Cylofold: 0.677 Mastr(20): 0.459 Positive Predictive Value Cylofold: 0.849 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.798 Mastr(seed): 0.406 Sensitivity Cylofold: 0.772 Mastr(seed): 0.212 Positive Predictive Value Cylofold: 0.828 Mastr(seed): 0.784 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.943 Multilign(seed): 0.572 Sensitivity Cylofold: 0.935 Multilign(seed): 0.532 Positive Predictive Value Cylofold: 0.951 Multilign(seed): 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.943 PPfold(seed): 0.656 Sensitivity Cylofold: 0.935 PPfold(seed): 0.532 Positive Predictive Value Cylofold: 0.951 PPfold(seed): 0.815 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.771 MCFold: 0.294 Sensitivity Cylofold: 0.749 MCFold: 0.323 Positive Predictive Value Cylofold: 0.799 MCFold: 0.284 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	286 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 CentroidAlifold(20): 0.723 Sensitivity PETfold_pre2.0(seed): 0.709 CentroidAlifold(20): 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.810 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.767 CentroidAlifold(20): 0.723 Sensitivity ContextFold: 0.726 CentroidAlifold(20): 0.595 Positive Predictive Value ContextFold: 0.811 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 CentroidAlifold(20): 0.765 Sensitivity CentroidAlifold(seed): 0.647 CentroidAlifold(20): 0.646 Positive Predictive Value CentroidAlifold(seed): 0.917 CentroidAlifold(20): 0.906 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.718 CentroidHomfold‑LAST: 0.703 Sensitivity CentroidAlifold(20): 0.562 CentroidHomfold‑LAST: 0.552 Positive Predictive Value CentroidAlifold(20): 0.917 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidAlifold(20): 0.718 Sensitivity TurboFold(20): 0.685 CentroidAlifold(20): 0.562 Positive Predictive Value TurboFold(20): 0.802 CentroidAlifold(20): 0.917 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 CentroidAlifold(20): 0.723 Sensitivity PETfold_pre2.0(20): 0.681 CentroidAlifold(20): 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.783 CentroidAlifold(20): 0.879 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.736 CentroidAlifold(20): 0.721 Sensitivity PPfold(20): 0.641 CentroidAlifold(20): 0.571 Positive Predictive Value PPfold(20): 0.846 CentroidAlifold(20): 0.911 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Cylofold: 0.756 Sensitivity CentroidAlifold(20): 0.752 Cylofold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.723 IPknot: 0.577 Sensitivity CentroidAlifold(20): 0.595 IPknot: 0.509 Positive Predictive Value CentroidAlifold(20): 0.879 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Pknots: 0.723 Sensitivity CentroidAlifold(20): 0.752 Pknots: 0.632 Positive Predictive Value CentroidAlifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.765 MXScarna(seed): 0.661 Sensitivity CentroidAlifold(20): 0.645 MXScarna(seed): 0.575 Positive Predictive Value CentroidAlifold(20): 0.907 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(20): 0.595 RNAalifold(20): 0.588 Positive Predictive Value CentroidAlifold(20): 0.879 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidFold: 0.539 Sensitivity CentroidAlifold(20): 0.597 CentroidFold: 0.474 Positive Predictive Value CentroidAlifold(20): 0.880 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Multilign(20): 0.651 Sensitivity CentroidAlifold(20): 0.562 Multilign(20): 0.591 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.756 RNAalifold(seed): 0.650 Sensitivity CentroidAlifold(20): 0.634 RNAalifold(seed): 0.519 Positive Predictive Value CentroidAlifold(20): 0.901 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 RNASampler(20): 0.553 Sensitivity CentroidAlifold(20): 0.546 RNASampler(20): 0.434 Positive Predictive Value CentroidAlifold(20): 0.857 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 MXScarna(20): 0.608 Sensitivity CentroidAlifold(20): 0.595 MXScarna(20): 0.550 Positive Predictive Value CentroidAlifold(20): 0.879 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Contrafold: 0.523 Sensitivity CentroidAlifold(20): 0.595 Contrafold: 0.504 Positive Predictive Value CentroidAlifold(20): 0.879 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.719 Murlet(20): 0.566 Sensitivity CentroidAlifold(20): 0.578 Murlet(20): 0.445 Positive Predictive Value CentroidAlifold(20): 0.894 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Sfold: 0.496 Sensitivity CentroidAlifold(20): 0.595 Sfold: 0.440 Positive Predictive Value CentroidAlifold(20): 0.879 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.723 ProbKnot: 0.473 Sensitivity CentroidAlifold(20): 0.595 ProbKnot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.879 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.723 MaxExpect: 0.478 Sensitivity CentroidAlifold(20): 0.595 MaxExpect: 0.464 Positive Predictive Value CentroidAlifold(20): 0.879 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.718 McQFold: 0.454 Sensitivity CentroidAlifold(20): 0.562 McQFold: 0.434 Positive Predictive Value CentroidAlifold(20): 0.917 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(20): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Fold: 0.445 Sensitivity CentroidAlifold(20): 0.595 Fold: 0.446 Positive Predictive Value CentroidAlifold(20): 0.879 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.782 PknotsRG: 0.482 Sensitivity CentroidAlifold(20): 0.667 PknotsRG: 0.474 Positive Predictive Value CentroidAlifold(20): 0.917 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 UNAFold: 0.459 Sensitivity CentroidAlifold(20): 0.595 UNAFold: 0.454 Positive Predictive Value CentroidAlifold(20): 0.879 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A CentroidAlifold(20): N/A Sensitivity TurboFold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value TurboFold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAsubopt: 0.520 Sensitivity CentroidAlifold(20): 0.562 RNAsubopt: 0.518 Positive Predictive Value CentroidAlifold(20): 0.917 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Afold: 0.453 Sensitivity CentroidAlifold(20): 0.597 Afold: 0.449 Positive Predictive Value CentroidAlifold(20): 0.879 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNASLOpt: 0.456 Sensitivity CentroidAlifold(20): 0.564 RNASLOpt: 0.421 Positive Predictive Value CentroidAlifold(20): 0.915 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RNAfold: 0.444 Sensitivity CentroidAlifold(20): 0.595 RNAfold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.879 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 HotKnots: 0.717 Sensitivity CentroidAlifold(20): 0.752 HotKnots: 0.639 Positive Predictive Value CentroidAlifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RDfolder: 0.664 Sensitivity CentroidAlifold(20): 0.752 RDfolder: 0.586 Positive Predictive Value CentroidAlifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.718 CMfinder(20): 0.482 Sensitivity CentroidAlifold(20): 0.562 CMfinder(20): 0.310 Positive Predictive Value CentroidAlifold(20): 0.917 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAshapes: 0.457 Sensitivity CentroidAlifold(20): 0.562 RNAshapes: 0.442 Positive Predictive Value CentroidAlifold(20): 0.917 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.762 CRWrnafold: 0.484 Sensitivity CentroidAlifold(20): 0.636 CRWrnafold: 0.476 Positive Predictive Value CentroidAlifold(20): 0.914 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Carnac(20): 0.496 Sensitivity CentroidAlifold(20): 0.595 Carnac(20): 0.277 Positive Predictive Value CentroidAlifold(20): 0.879 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Vsfold5: 0.371 Sensitivity CentroidAlifold(20): 0.563 Vsfold5: 0.344 Positive Predictive Value CentroidAlifold(20): 0.917 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Vsfold4: 0.392 Sensitivity CentroidAlifold(20): 0.563 Vsfold4: 0.355 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAwolf: 0.368 Sensitivity CentroidAlifold(20): 0.562 RNAwolf: 0.378 Positive Predictive Value CentroidAlifold(20): 0.917 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.897 Carnac(seed): 0.552 Sensitivity CentroidAlifold(20): 0.852 Carnac(seed): 0.327 Positive Predictive Value CentroidAlifold(20): 0.945 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RSpredict(20): 0.425 Sensitivity CentroidAlifold(20): 0.595 RSpredict(20): 0.345 Positive Predictive Value CentroidAlifold(20): 0.879 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Alterna: 0.656 Sensitivity CentroidAlifold(20): 0.752 Alterna: 0.602 Positive Predictive Value CentroidAlifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.713 NanoFolder: 0.152 Sensitivity CentroidAlifold(20): 0.562 NanoFolder: 0.174 Positive Predictive Value CentroidAlifold(20): 0.906 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.761 RSpredict(seed): 0.402 Sensitivity CentroidAlifold(20): 0.638 RSpredict(seed): 0.269 Positive Predictive Value CentroidAlifold(20): 0.907 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.646 Mastr(20): 0.035 Sensitivity CentroidAlifold(20): 0.493 Mastr(20): 0.002 Positive Predictive Value CentroidAlifold(20): 0.847 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.555 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.925 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(seed): N/A CentroidAlifold(20): N/A Sensitivity PPfold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value PPfold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MCFold: 0.291 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.323 Positive Predictive Value CentroidAlifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
IPknot	610 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 IPknot: 0.573 Sensitivity PETfold_pre2.0(seed): 0.651 IPknot: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.790 IPknot: 0.646 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.678 IPknot: 0.538 Sensitivity ContextFold: 0.636 IPknot: 0.470 Positive Predictive Value ContextFold: 0.724 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 IPknot: 0.611 Sensitivity CentroidAlifold(seed): 0.615 IPknot: 0.536 Positive Predictive Value CentroidAlifold(seed): 0.906 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 IPknot: 0.603 Sensitivity CentroidHomfold‑LAST: 0.468 IPknot: 0.546 Positive Predictive Value CentroidHomfold‑LAST: 0.870 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.741 IPknot: 0.649 Sensitivity TurboFold(20): 0.685 IPknot: 0.575 Positive Predictive Value TurboFold(20): 0.802 IPknot: 0.734 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 IPknot: 0.577 Sensitivity PETfold_pre2.0(20): 0.681 IPknot: 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.783 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.736 IPknot: 0.638 Sensitivity PPfold(20): 0.641 IPknot: 0.562 Positive Predictive Value PPfold(20): 0.846 IPknot: 0.725 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs IPknot Matthews Correlation Coefficient Cylofold: 0.701 IPknot: 0.569 Sensitivity Cylofold: 0.673 IPknot: 0.511 Positive Predictive Value Cylofold: 0.734 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.723 IPknot: 0.577 Sensitivity CentroidAlifold(20): 0.595 IPknot: 0.509 Positive Predictive Value CentroidAlifold(20): 0.879 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Pknots vs IPknot Matthews Correlation Coefficient Pknots: 0.697 IPknot: 0.558 Sensitivity Pknots: 0.668 IPknot: 0.501 Positive Predictive Value Pknots: 0.733 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.628 IPknot: 0.611 Sensitivity MXScarna(seed): 0.533 IPknot: 0.537 Positive Predictive Value MXScarna(seed): 0.741 IPknot: 0.697 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.668 IPknot: 0.577 Sensitivity RNAalifold(20): 0.588 IPknot: 0.509 Positive Predictive Value RNAalifold(20): 0.760 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.535 CentroidFold: 0.505 Sensitivity IPknot: 0.467 CentroidFold: 0.441 Positive Predictive Value IPknot: 0.613 CentroidFold: 0.579 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.655 IPknot: 0.604 Sensitivity RNASampler(seed): 0.572 IPknot: 0.537 Positive Predictive Value RNASampler(seed): 0.755 IPknot: 0.686 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	= Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.651 IPknot: 0.649 Sensitivity Multilign(20): 0.591 IPknot: 0.576 Positive Predictive Value Multilign(20): 0.718 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 0.231589081714	- RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.629 IPknot: 0.604 Sensitivity RNAalifold(seed): 0.485 IPknot: 0.530 Positive Predictive Value RNAalifold(seed): 0.816 IPknot: 0.689 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.589 RNASampler(20): 0.553 Sensitivity IPknot: 0.521 RNASampler(20): 0.434 Positive Predictive Value IPknot: 0.668 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.608 IPknot: 0.577 Sensitivity MXScarna(20): 0.550 IPknot: 0.509 Positive Predictive Value MXScarna(20): 0.674 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.538 Contrafold: 0.497 Sensitivity IPknot: 0.470 Contrafold: 0.478 Positive Predictive Value IPknot: 0.616 Contrafold: 0.517 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.622 Murlet(20): 0.566 Sensitivity IPknot: 0.548 Murlet(20): 0.445 Positive Predictive Value IPknot: 0.707 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.538 Sfold: 0.452 Sensitivity IPknot: 0.470 Sfold: 0.401 Positive Predictive Value IPknot: 0.616 Sfold: 0.510 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.538 ProbKnot: 0.443 Sensitivity IPknot: 0.470 ProbKnot: 0.438 Positive Predictive Value IPknot: 0.616 ProbKnot: 0.449 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.538 MaxExpect: 0.448 Sensitivity IPknot: 0.470 MaxExpect: 0.435 Positive Predictive Value IPknot: 0.616 MaxExpect: 0.462 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.597 McQFold: 0.450 Sensitivity IPknot: 0.539 McQFold: 0.440 Positive Predictive Value IPknot: 0.664 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs IPknot Matthews Correlation Coefficient Murlet(seed): 0.584 IPknot: 0.543 Sensitivity Murlet(seed): 0.492 IPknot: 0.466 Positive Predictive Value Murlet(seed): 0.694 IPknot: 0.633 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.23236503487e-06	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.538 Fold: 0.418 Sensitivity IPknot: 0.470 Fold: 0.421 Positive Predictive Value IPknot: 0.616 Fold: 0.415 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.559 PknotsRG: 0.428 Sensitivity IPknot: 0.488 PknotsRG: 0.427 Positive Predictive Value IPknot: 0.642 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.538 UNAFold: 0.415 Sensitivity IPknot: 0.470 UNAFold: 0.412 Positive Predictive Value IPknot: 0.616 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.646 TurboFold(seed): 0.633 Sensitivity IPknot: 0.592 TurboFold(seed): 0.562 Positive Predictive Value IPknot: 0.708 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.01818206431e-06	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.603 RNAsubopt: 0.473 Sensitivity IPknot: 0.546 RNAsubopt: 0.480 Positive Predictive Value IPknot: 0.667 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.534 Afold: 0.409 Sensitivity IPknot: 0.462 Afold: 0.407 Positive Predictive Value IPknot: 0.618 Afold: 0.412 Number of pairs reference - predicted secondary structure: 594 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.599 RNASLOpt: 0.445 Sensitivity IPknot: 0.539 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.666 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.538 RNAfold: 0.408 Sensitivity IPknot: 0.470 RNAfold: 0.409 Positive Predictive Value IPknot: 0.616 RNAfold: 0.407 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.489 HotKnots: 0.453 Sensitivity IPknot: 0.435 HotKnots: 0.445 Positive Predictive Value IPknot: 0.556 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.558 RDfolder: 0.508 Sensitivity IPknot: 0.501 RDfolder: 0.432 Positive Predictive Value IPknot: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.649 CMfinder(20): 0.482 Sensitivity IPknot: 0.575 CMfinder(20): 0.310 Positive Predictive Value IPknot: 0.734 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.602 RNAshapes: 0.408 Sensitivity IPknot: 0.543 RNAshapes: 0.404 Positive Predictive Value IPknot: 0.668 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.556 CRWrnafold: 0.395 Sensitivity IPknot: 0.486 CRWrnafold: 0.398 Positive Predictive Value IPknot: 0.637 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.577 Carnac(20): 0.496 Sensitivity IPknot: 0.509 Carnac(20): 0.277 Positive Predictive Value IPknot: 0.654 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.601 Vsfold5: 0.333 Sensitivity IPknot: 0.543 Vsfold5: 0.317 Positive Predictive Value IPknot: 0.667 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.601 Vsfold4: 0.337 Sensitivity IPknot: 0.543 Vsfold4: 0.310 Positive Predictive Value IPknot: 0.666 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.567 RNAwolf: 0.302 Sensitivity IPknot: 0.499 RNAwolf: 0.316 Positive Predictive Value IPknot: 0.646 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.623 CMfinder(seed): 0.363 Sensitivity IPknot: 0.563 CMfinder(seed): 0.184 Positive Predictive Value IPknot: 0.690 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.588 Carnac(seed): 0.253 Sensitivity IPknot: 0.539 Carnac(seed): 0.068 Positive Predictive Value IPknot: 0.643 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.577 RSpredict(20): 0.425 Sensitivity IPknot: 0.509 RSpredict(20): 0.345 Positive Predictive Value IPknot: 0.654 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.558 Alterna: 0.393 Sensitivity IPknot: 0.501 Alterna: 0.365 Positive Predictive Value IPknot: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.628 NanoFolder: 0.174 Sensitivity IPknot: 0.565 NanoFolder: 0.207 Positive Predictive Value IPknot: 0.700 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.609 RSpredict(seed): 0.363 Sensitivity IPknot: 0.535 RSpredict(seed): 0.222 Positive Predictive Value IPknot: 0.694 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.549 Mastr(20): 0.035 Sensitivity IPknot: 0.485 Mastr(20): 0.002 Positive Predictive Value IPknot: 0.622 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.629 Mastr(seed): 0.040 Sensitivity IPknot: 0.557 Mastr(seed): 0.002 Positive Predictive Value IPknot: 0.711 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.684 Multilign(seed): 0.575 Sensitivity IPknot: 0.586 Multilign(seed): 0.536 Positive Predictive Value IPknot: 0.804 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.684 PPfold(seed): 0.666 Sensitivity IPknot: 0.586 PPfold(seed): 0.536 Positive Predictive Value IPknot: 0.804 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.503 MCFold: 0.290 Sensitivity IPknot: 0.457 MCFold: 0.320 Positive Predictive Value IPknot: 0.562 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Pknots	18 Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: 0.781 PETfold_pre2.0(seed): 0.736 Sensitivity Pknots: 0.760 PETfold_pre2.0(seed): 0.661 Positive Predictive Value Pknots: 0.808 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.55268413083e-08	46 Pknots vs ContextFold Matthews Correlation Coefficient Pknots: 0.697 ContextFold: 0.500 Sensitivity Pknots: 0.668 ContextFold: 0.441 Positive Predictive Value Pknots: 0.733 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Pknots: 0.768 Sensitivity CentroidAlifold(seed): 0.642 Pknots: 0.748 Positive Predictive Value CentroidAlifold(seed): 0.936 Pknots: 0.792 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.453544033954	46 Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: 0.697 CentroidHomfold‑LAST: 0.541 Sensitivity Pknots: 0.668 CentroidHomfold‑LAST: 0.471 Positive Predictive Value Pknots: 0.733 CentroidHomfold‑LAST: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.857 Pknots: 0.723 Sensitivity TurboFold(20): 0.744 Pknots: 0.632 Positive Predictive Value TurboFold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Pknots: 0.723 Sensitivity PETfold_pre2.0(20): 0.759 Pknots: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.962 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.840 Pknots: 0.723 Sensitivity PPfold(20): 0.737 Pknots: 0.632 Positive Predictive Value PPfold(20): 0.961 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	45 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.764 Pknots: 0.691 Sensitivity Cylofold: 0.742 Pknots: 0.662 Positive Predictive Value Cylofold: 0.791 Pknots: 0.728 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Pknots: 0.723 Sensitivity CentroidAlifold(20): 0.752 Pknots: 0.632 Positive Predictive Value CentroidAlifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 Pknots vs IPknot Matthews Correlation Coefficient Pknots: 0.697 IPknot: 0.558 Sensitivity Pknots: 0.668 IPknot: 0.501 Positive Predictive Value Pknots: 0.733 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: 0.768 MXScarna(seed): 0.514 Sensitivity Pknots: 0.748 MXScarna(seed): 0.481 Positive Predictive Value Pknots: 0.792 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	? RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.844 Pknots: 0.723 Sensitivity RNAalifold(20): 0.722 Pknots: 0.632 Positive Predictive Value RNAalifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: 0.697 CentroidFold: 0.544 Sensitivity Pknots: 0.668 CentroidFold: 0.485 Positive Predictive Value Pknots: 0.733 CentroidFold: 0.621 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.803 RNASampler(seed): 0.641 Sensitivity Pknots: 0.820 RNASampler(seed): 0.562 Positive Predictive Value Pknots: 0.789 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.35333035499e-09	? Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.862 Pknots: 0.723 Sensitivity Multilign(20): 0.752 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.768 RNAalifold(seed): 0.651 Sensitivity Pknots: 0.748 RNAalifold(seed): 0.519 Positive Predictive Value Pknots: 0.792 RNAalifold(seed): 0.823 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.16131455263e-08	? RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.840 Pknots: 0.723 Sensitivity RNASampler(20): 0.714 Pknots: 0.632 Positive Predictive Value RNASampler(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.837 Pknots: 0.723 Sensitivity MXScarna(20): 0.752 Pknots: 0.632 Positive Predictive Value MXScarna(20): 0.935 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Contrafold Matthews Correlation Coefficient Pknots: 0.697 Contrafold: 0.515 Sensitivity Pknots: 0.668 Contrafold: 0.477 Positive Predictive Value Pknots: 0.733 Contrafold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.741 Pknots: 0.723 Sensitivity Murlet(20): 0.594 Pknots: 0.632 Positive Predictive Value Murlet(20): 0.929 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.697 Sfold: 0.482 Sensitivity Pknots: 0.668 Sfold: 0.435 Positive Predictive Value Pknots: 0.733 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.697 ProbKnot: 0.527 Sensitivity Pknots: 0.668 ProbKnot: 0.496 Positive Predictive Value Pknots: 0.733 ProbKnot: 0.570 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MaxExpect Matthews Correlation Coefficient Pknots: 0.697 MaxExpect: 0.503 Sensitivity Pknots: 0.668 MaxExpect: 0.463 Positive Predictive Value Pknots: 0.733 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	- McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.705 Pknots: 0.697 Sensitivity McQFold: 0.679 Pknots: 0.668 Positive Predictive Value McQFold: 0.738 Pknots: 0.733 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.68360786394e-05	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.803 Murlet(seed): 0.432 Sensitivity Pknots: 0.820 Murlet(seed): 0.283 Positive Predictive Value Pknots: 0.789 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.697 Fold: 0.504 Sensitivity Pknots: 0.668 Fold: 0.466 Positive Predictive Value Pknots: 0.733 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.697 PknotsRG: 0.627 Sensitivity Pknots: 0.668 PknotsRG: 0.601 Positive Predictive Value Pknots: 0.733 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.697 UNAFold: 0.468 Sensitivity Pknots: 0.668 UNAFold: 0.431 Positive Predictive Value Pknots: 0.733 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.870 TurboFold(seed): 0.600 Sensitivity Pknots: 0.887 TurboFold(seed): 0.518 Positive Predictive Value Pknots: 0.856 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.697 RNAsubopt: 0.470 Sensitivity Pknots: 0.668 RNAsubopt: 0.435 Positive Predictive Value Pknots: 0.733 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.653 Afold: 0.309 Sensitivity Pknots: 0.630 Afold: 0.296 Positive Predictive Value Pknots: 0.684 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.697 RNASLOpt: 0.549 Sensitivity Pknots: 0.668 RNASLOpt: 0.489 Positive Predictive Value Pknots: 0.733 RNASLOpt: 0.626 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.697 RNAfold: 0.476 Sensitivity Pknots: 0.668 RNAfold: 0.439 Positive Predictive Value Pknots: 0.733 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.697 HotKnots: 0.534 Sensitivity Pknots: 0.668 HotKnots: 0.510 Positive Predictive Value Pknots: 0.733 HotKnots: 0.569 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.508 Sensitivity Pknots: 0.668 RDfolder: 0.432 Positive Predictive Value Pknots: 0.733 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.779 Pknots: 0.723 Sensitivity CMfinder(20): 0.617 Pknots: 0.632 Positive Predictive Value CMfinder(20): 0.988 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.697 RNAshapes: 0.463 Sensitivity Pknots: 0.668 RNAshapes: 0.426 Positive Predictive Value Pknots: 0.733 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.697 CRWrnafold: 0.458 Sensitivity Pknots: 0.668 CRWrnafold: 0.415 Positive Predictive Value Pknots: 0.733 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.821 Pknots: 0.723 Sensitivity Carnac(20): 0.684 Pknots: 0.632 Positive Predictive Value Carnac(20): 0.989 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.697 Vsfold5: 0.597 Sensitivity Pknots: 0.668 Vsfold5: 0.550 Positive Predictive Value Pknots: 0.733 Vsfold5: 0.657 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.697 Vsfold4: 0.480 Sensitivity Pknots: 0.668 Vsfold4: 0.423 Positive Predictive Value Pknots: 0.733 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.697 RNAwolf: 0.401 Sensitivity Pknots: 0.668 RNAwolf: 0.381 Positive Predictive Value Pknots: 0.733 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: 0.767 CMfinder(seed): 0.459 Sensitivity Pknots: 0.787 CMfinder(seed): 0.365 Positive Predictive Value Pknots: 0.752 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.803 Carnac(seed): 0.531 Sensitivity Pknots: 0.820 Carnac(seed): 0.292 Positive Predictive Value Pknots: 0.789 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.95953827463e-09	? Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.723 RSpredict(20): 0.672 Sensitivity Pknots: 0.632 RSpredict(20): 0.549 Positive Predictive Value Pknots: 0.832 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.697 Alterna: 0.393 Sensitivity Pknots: 0.668 Alterna: 0.365 Positive Predictive Value Pknots: 0.733 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.808 NanoFolder: 0.304 Sensitivity Pknots: 0.759 NanoFolder: 0.343 Positive Predictive Value Pknots: 0.863 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.768 RSpredict(seed): 0.518 Sensitivity Pknots: 0.748 RSpredict(seed): 0.437 Positive Predictive Value Pknots: 0.792 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.71568867205e-08	? Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.723 Mastr(20): 0.561 Sensitivity Pknots: 0.632 Mastr(20): 0.459 Positive Predictive Value Pknots: 0.832 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.768 Mastr(seed): 0.365 Sensitivity Pknots: 0.748 Mastr(seed): 0.202 Positive Predictive Value Pknots: 0.792 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.96907987703e-08	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.886 Multilign(seed): 0.575 Sensitivity Pknots: 0.893 Multilign(seed): 0.536 Positive Predictive Value Pknots: 0.880 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.886 PPfold(seed): 0.666 Sensitivity Pknots: 0.893 PPfold(seed): 0.536 Positive Predictive Value Pknots: 0.880 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.707 MCFold: 0.296 Sensitivity Pknots: 0.676 MCFold: 0.325 Positive Predictive Value Pknots: 0.747 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	363 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.762 MXScarna(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.703 MXScarna(seed): 0.533 Positive Predictive Value PETfold_pre2.0(seed): 0.826 MXScarna(seed): 0.741 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.815 MXScarna(seed): 0.628 Sensitivity ContextFold: 0.769 MXScarna(seed): 0.533 Positive Predictive Value ContextFold: 0.864 MXScarna(seed): 0.741 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 MXScarna(seed): 0.628 Sensitivity CentroidAlifold(seed): 0.615 MXScarna(seed): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.906 MXScarna(seed): 0.740 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 MXScarna(seed): 0.598 Sensitivity CentroidHomfold‑LAST: 0.509 MXScarna(seed): 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	168 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 MXScarna(seed): 0.656 Sensitivity TurboFold(20): 0.703 MXScarna(seed): 0.543 Positive Predictive Value TurboFold(20): 0.823 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	226 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.774 MXScarna(seed): 0.661 Sensitivity PETfold_pre2.0(20): 0.724 MXScarna(seed): 0.575 Positive Predictive Value PETfold_pre2.0(20): 0.827 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	165 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.760 MXScarna(seed): 0.665 Sensitivity PPfold(20): 0.668 MXScarna(seed): 0.553 Positive Predictive Value PPfold(20): 0.865 MXScarna(seed): 0.799 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.798 MXScarna(seed): 0.542 Sensitivity Cylofold: 0.772 MXScarna(seed): 0.505 Positive Predictive Value Cylofold: 0.828 MXScarna(seed): 0.590 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	226 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.765 MXScarna(seed): 0.661 Sensitivity CentroidAlifold(20): 0.645 MXScarna(seed): 0.575 Positive Predictive Value CentroidAlifold(20): 0.907 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.628 IPknot: 0.611 Sensitivity MXScarna(seed): 0.533 IPknot: 0.537 Positive Predictive Value MXScarna(seed): 0.741 IPknot: 0.697 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: 0.768 MXScarna(seed): 0.514 Sensitivity Pknots: 0.748 MXScarna(seed): 0.481 Positive Predictive Value Pknots: 0.792 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08		- RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.722 MXScarna(seed): 0.661 Sensitivity RNAalifold(20): 0.637 MXScarna(seed): 0.575 Positive Predictive Value RNAalifold(20): 0.817 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.630 CentroidFold: 0.575 Sensitivity MXScarna(seed): 0.534 CentroidFold: 0.505 Positive Predictive Value MXScarna(seed): 0.744 CentroidFold: 0.656 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 MXScarna(seed): 0.440 Sensitivity RNASampler(seed): 0.572 MXScarna(seed): 0.421 Positive Predictive Value RNASampler(seed): 0.755 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	- Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.659 MXScarna(seed): 0.655 Sensitivity Multilign(20): 0.595 MXScarna(seed): 0.540 Positive Predictive Value Multilign(20): 0.730 MXScarna(seed): 0.796 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 2.23046259944e-06	- RNAalifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.636 MXScarna(seed): 0.628 Sensitivity RNAalifold(seed): 0.489 MXScarna(seed): 0.533 Positive Predictive Value RNAalifold(seed): 0.827 MXScarna(seed): 0.740 Number of pairs reference - predicted secondary structure: 359 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.605 RNASampler(20): 0.526 Sensitivity MXScarna(seed): 0.485 RNASampler(20): 0.384 Positive Predictive Value MXScarna(seed): 0.757 RNASampler(20): 0.723 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 MXScarna(20): 0.650 Sensitivity MXScarna(seed): 0.575 MXScarna(20): 0.581 Positive Predictive Value MXScarna(seed): 0.761 MXScarna(20): 0.727 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.628 Contrafold: 0.559 Sensitivity MXScarna(seed): 0.533 Contrafold: 0.535 Positive Predictive Value MXScarna(seed): 0.741 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Murlet(20): 0.566 Sensitivity MXScarna(seed): 0.557 Murlet(20): 0.437 Positive Predictive Value MXScarna(seed): 0.770 Murlet(20): 0.734 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.628 Sfold: 0.536 Sensitivity MXScarna(seed): 0.533 Sfold: 0.475 Positive Predictive Value MXScarna(seed): 0.741 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.628 ProbKnot: 0.510 Sensitivity MXScarna(seed): 0.533 ProbKnot: 0.495 Positive Predictive Value MXScarna(seed): 0.741 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.628 MaxExpect: 0.513 Sensitivity MXScarna(seed): 0.533 MaxExpect: 0.495 Positive Predictive Value MXScarna(seed): 0.741 MaxExpect: 0.533 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.594 McQFold: 0.486 Sensitivity MXScarna(seed): 0.475 McQFold: 0.465 Positive Predictive Value MXScarna(seed): 0.744 McQFold: 0.509 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.614 Murlet(seed): 0.584 Sensitivity MXScarna(seed): 0.576 Murlet(seed): 0.492 Positive Predictive Value MXScarna(seed): 0.656 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10387130242e-07	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.628 Fold: 0.481 Sensitivity MXScarna(seed): 0.533 Fold: 0.478 Positive Predictive Value MXScarna(seed): 0.741 Fold: 0.485 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.644 PknotsRG: 0.488 Sensitivity MXScarna(seed): 0.543 PknotsRG: 0.480 Positive Predictive Value MXScarna(seed): 0.766 PknotsRG: 0.497 Number of pairs reference - predicted secondary structure: 351 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.628 UNAFold: 0.497 Sensitivity MXScarna(seed): 0.533 UNAFold: 0.487 Positive Predictive Value MXScarna(seed): 0.741 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 MXScarna(seed): 0.505 Sensitivity TurboFold(seed): 0.562 MXScarna(seed): 0.472 Positive Predictive Value TurboFold(seed): 0.716 MXScarna(seed): 0.545 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.85673856424e-11	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.598 RNAsubopt: 0.535 Sensitivity MXScarna(seed): 0.480 RNAsubopt: 0.532 Positive Predictive Value MXScarna(seed): 0.747 RNAsubopt: 0.539 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.629 Afold: 0.484 Sensitivity MXScarna(seed): 0.535 Afold: 0.475 Positive Predictive Value MXScarna(seed): 0.741 Afold: 0.494 Number of pairs reference - predicted secondary structure: 309 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.617 RNASLOpt: 0.478 Sensitivity MXScarna(seed): 0.500 RNASLOpt: 0.440 Positive Predictive Value MXScarna(seed): 0.763 RNASLOpt: 0.521 Number of pairs reference - predicted secondary structure: 250 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.628 RNAfold: 0.478 Sensitivity MXScarna(seed): 0.533 RNAfold: 0.471 Positive Predictive Value MXScarna(seed): 0.741 RNAfold: 0.485 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.603 MXScarna(seed): 0.539 Sensitivity HotKnots: 0.588 MXScarna(seed): 0.501 Positive Predictive Value HotKnots: 0.624 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	- RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: 0.616 MXScarna(seed): 0.514 Sensitivity RDfolder: 0.531 MXScarna(seed): 0.481 Positive Predictive Value RDfolder: 0.721 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.656 CMfinder(20): 0.505 Sensitivity MXScarna(seed): 0.543 CMfinder(20): 0.331 Positive Predictive Value MXScarna(seed): 0.795 CMfinder(20): 0.770 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.603 RNAshapes: 0.486 Sensitivity MXScarna(seed): 0.485 RNAshapes: 0.470 Positive Predictive Value MXScarna(seed): 0.751 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.629 CRWrnafold: 0.477 Sensitivity MXScarna(seed): 0.522 CRWrnafold: 0.469 Positive Predictive Value MXScarna(seed): 0.759 CRWrnafold: 0.486 Number of pairs reference - predicted secondary structure: 328 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 Carnac(20): 0.511 Sensitivity MXScarna(seed): 0.575 Carnac(20): 0.288 Positive Predictive Value MXScarna(seed): 0.761 Carnac(20): 0.909 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.603 Vsfold5: 0.382 Sensitivity MXScarna(seed): 0.485 Vsfold5: 0.352 Positive Predictive Value MXScarna(seed): 0.751 Vsfold5: 0.417 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.605 Vsfold4: 0.407 Sensitivity MXScarna(seed): 0.488 Vsfold4: 0.367 Positive Predictive Value MXScarna(seed): 0.752 Vsfold4: 0.454 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.594 RNAwolf: 0.374 Sensitivity MXScarna(seed): 0.475 RNAwolf: 0.382 Positive Predictive Value MXScarna(seed): 0.744 RNAwolf: 0.368 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 MXScarna(seed): 0.307 Sensitivity CMfinder(seed): 0.184 MXScarna(seed): 0.199 Positive Predictive Value CMfinder(seed): 0.716 MXScarna(seed): 0.476 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.533 Carnac(seed): 0.253 Sensitivity MXScarna(seed): 0.405 Carnac(seed): 0.068 Positive Predictive Value MXScarna(seed): 0.703 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 RSpredict(20): 0.498 Sensitivity MXScarna(seed): 0.575 RSpredict(20): 0.391 Positive Predictive Value MXScarna(seed): 0.761 RSpredict(20): 0.635 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.514 Alterna: 0.486 Sensitivity MXScarna(seed): 0.481 Alterna: 0.455 Positive Predictive Value MXScarna(seed): 0.558 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.47710327474e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.586 NanoFolder: 0.184 Sensitivity MXScarna(seed): 0.470 NanoFolder: 0.210 Positive Predictive Value MXScarna(seed): 0.731 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.627 RSpredict(seed): 0.364 Sensitivity MXScarna(seed): 0.531 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.741 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.616 Mastr(20): 0.049 Sensitivity MXScarna(seed): 0.522 Mastr(20): 0.003 Positive Predictive Value MXScarna(seed): 0.728 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 177 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.582 Mastr(seed): 0.041 Sensitivity MXScarna(seed): 0.469 Mastr(seed): 0.002 Positive Predictive Value MXScarna(seed): 0.723 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 MXScarna(seed): 0.468 Sensitivity Multilign(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value Multilign(seed): 0.625 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 MXScarna(seed): 0.468 Sensitivity PPfold(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value PPfold(seed): 0.833 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.538 MCFold: 0.358 Sensitivity MXScarna(seed): 0.502 MCFold: 0.409 Positive Predictive Value MXScarna(seed): 0.586 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.70887622364e-08
RNAalifold(20)	286 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 RNAalifold(20): 0.668 Sensitivity PETfold_pre2.0(seed): 0.709 RNAalifold(20): 0.588 Positive Predictive Value PETfold_pre2.0(seed): 0.810 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.767 RNAalifold(20): 0.668 Sensitivity ContextFold: 0.726 RNAalifold(20): 0.588 Positive Predictive Value ContextFold: 0.811 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 RNAalifold(20): 0.722 Sensitivity CentroidAlifold(seed): 0.647 RNAalifold(20): 0.638 Positive Predictive Value CentroidAlifold(seed): 0.917 RNAalifold(20): 0.817 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 RNAalifold(20): 0.661 Sensitivity CentroidHomfold‑LAST: 0.552 RNAalifold(20): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.741 RNAalifold(20): 0.661 Sensitivity TurboFold(20): 0.685 RNAalifold(20): 0.533 Positive Predictive Value TurboFold(20): 0.802 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RNAalifold(20): 0.668 Sensitivity PETfold_pre2.0(20): 0.681 RNAalifold(20): 0.588 Positive Predictive Value PETfold_pre2.0(20): 0.783 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.736 RNAalifold(20): 0.664 Sensitivity PPfold(20): 0.641 RNAalifold(20): 0.545 Positive Predictive Value PPfold(20): 0.846 RNAalifold(20): 0.808 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.844 Cylofold: 0.756 Sensitivity RNAalifold(20): 0.722 Cylofold: 0.677 Positive Predictive Value RNAalifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	286 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(20): 0.595 RNAalifold(20): 0.588 Positive Predictive Value CentroidAlifold(20): 0.879 RNAalifold(20): 0.760 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.668 IPknot: 0.577 Sensitivity RNAalifold(20): 0.588 IPknot: 0.509 Positive Predictive Value RNAalifold(20): 0.760 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.844 Pknots: 0.723 Sensitivity RNAalifold(20): 0.722 Pknots: 0.632 Positive Predictive Value RNAalifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	226 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.722 MXScarna(seed): 0.661 Sensitivity RNAalifold(20): 0.637 MXScarna(seed): 0.575 Positive Predictive Value RNAalifold(20): 0.817 MXScarna(seed): 0.761 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.671 CentroidFold: 0.539 Sensitivity RNAalifold(20): 0.591 CentroidFold: 0.474 Positive Predictive Value RNAalifold(20): 0.762 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Multilign(20): 0.651 Sensitivity RNAalifold(20): 0.532 Multilign(20): 0.591 Positive Predictive Value RNAalifold(20): 0.821 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.709 RNAalifold(seed): 0.650 Sensitivity RNAalifold(20): 0.626 RNAalifold(seed): 0.519 Positive Predictive Value RNAalifold(20): 0.803 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.632 RNASampler(20): 0.553 Sensitivity RNAalifold(20): 0.526 RNASampler(20): 0.434 Positive Predictive Value RNAalifold(20): 0.760 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 MXScarna(20): 0.608 Sensitivity RNAalifold(20): 0.588 MXScarna(20): 0.550 Positive Predictive Value RNAalifold(20): 0.760 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.668 Contrafold: 0.523 Sensitivity RNAalifold(20): 0.588 Contrafold: 0.504 Positive Predictive Value RNAalifold(20): 0.760 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.666 Murlet(20): 0.566 Sensitivity RNAalifold(20): 0.560 Murlet(20): 0.445 Positive Predictive Value RNAalifold(20): 0.793 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.668 Sfold: 0.496 Sensitivity RNAalifold(20): 0.588 Sfold: 0.440 Positive Predictive Value RNAalifold(20): 0.760 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.668 ProbKnot: 0.473 Sensitivity RNAalifold(20): 0.588 ProbKnot: 0.463 Positive Predictive Value RNAalifold(20): 0.760 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.668 MaxExpect: 0.478 Sensitivity RNAalifold(20): 0.588 MaxExpect: 0.464 Positive Predictive Value RNAalifold(20): 0.760 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.661 McQFold: 0.454 Sensitivity RNAalifold(20): 0.533 McQFold: 0.434 Positive Predictive Value RNAalifold(20): 0.820 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Murlet(seed): N/A Sensitivity RNAalifold(20): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.668 Fold: 0.445 Sensitivity RNAalifold(20): 0.588 Fold: 0.446 Positive Predictive Value RNAalifold(20): 0.760 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.744 PknotsRG: 0.482 Sensitivity RNAalifold(20): 0.655 PknotsRG: 0.474 Positive Predictive Value RNAalifold(20): 0.846 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.668 UNAFold: 0.459 Sensitivity RNAalifold(20): 0.588 UNAFold: 0.454 Positive Predictive Value RNAalifold(20): 0.760 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A RNAalifold(20): N/A Sensitivity TurboFold(seed): N/A RNAalifold(20): N/A Positive Predictive Value TurboFold(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.661 RNAsubopt: 0.520 Sensitivity RNAalifold(20): 0.533 RNAsubopt: 0.518 Positive Predictive Value RNAalifold(20): 0.820 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.671 Afold: 0.453 Sensitivity RNAalifold(20): 0.592 Afold: 0.449 Positive Predictive Value RNAalifold(20): 0.760 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.663 RNASLOpt: 0.456 Sensitivity RNAalifold(20): 0.537 RNASLOpt: 0.421 Positive Predictive Value RNAalifold(20): 0.819 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAfold: 0.444 Sensitivity RNAalifold(20): 0.588 RNAfold: 0.443 Positive Predictive Value RNAalifold(20): 0.760 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.844 HotKnots: 0.717 Sensitivity RNAalifold(20): 0.722 HotKnots: 0.639 Positive Predictive Value RNAalifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.844 RDfolder: 0.664 Sensitivity RNAalifold(20): 0.722 RDfolder: 0.586 Positive Predictive Value RNAalifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.661 CMfinder(20): 0.482 Sensitivity RNAalifold(20): 0.533 CMfinder(20): 0.310 Positive Predictive Value RNAalifold(20): 0.820 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.663 RNAshapes: 0.457 Sensitivity RNAalifold(20): 0.535 RNAshapes: 0.442 Positive Predictive Value RNAalifold(20): 0.823 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.723 CRWrnafold: 0.484 Sensitivity RNAalifold(20): 0.622 CRWrnafold: 0.476 Positive Predictive Value RNAalifold(20): 0.841 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Carnac(20): 0.496 Sensitivity RNAalifold(20): 0.588 Carnac(20): 0.277 Positive Predictive Value RNAalifold(20): 0.760 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.663 Vsfold5: 0.371 Sensitivity RNAalifold(20): 0.536 Vsfold5: 0.344 Positive Predictive Value RNAalifold(20): 0.821 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.662 Vsfold4: 0.392 Sensitivity RNAalifold(20): 0.535 Vsfold4: 0.355 Positive Predictive Value RNAalifold(20): 0.821 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.661 RNAwolf: 0.368 Sensitivity RNAalifold(20): 0.533 RNAwolf: 0.378 Positive Predictive Value RNAalifold(20): 0.820 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 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	? RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.807 Carnac(seed): 0.552 Sensitivity RNAalifold(20): 0.745 Carnac(seed): 0.327 Positive Predictive Value RNAalifold(20): 0.874 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(20): 0.425 Sensitivity RNAalifold(20): 0.588 RSpredict(20): 0.345 Positive Predictive Value RNAalifold(20): 0.760 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.844 Alterna: 0.656 Sensitivity RNAalifold(20): 0.722 Alterna: 0.602 Positive Predictive Value RNAalifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.660 NanoFolder: 0.152 Sensitivity RNAalifold(20): 0.538 NanoFolder: 0.174 Positive Predictive Value RNAalifold(20): 0.811 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.715 RSpredict(seed): 0.402 Sensitivity RNAalifold(20): 0.629 RSpredict(seed): 0.269 Positive Predictive Value RNAalifold(20): 0.814 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.571 Mastr(20): 0.035 Sensitivity RNAalifold(20): 0.478 Mastr(20): 0.002 Positive Predictive Value RNAalifold(20): 0.683 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.653 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.526 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.811 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): N/A PPfold(seed): N/A Sensitivity RNAalifold(20): N/A PPfold(seed): N/A Positive Predictive Value RNAalifold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.844 MCFold: 0.291 Sensitivity RNAalifold(20): 0.722 MCFold: 0.323 Positive Predictive Value RNAalifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
CentroidFold	609 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.718 CentroidFold: 0.537 Sensitivity PETfold_pre2.0(seed): 0.652 CentroidFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.791 CentroidFold: 0.607 Number of pairs reference - predicted secondary structure: 609 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.699 CentroidFold: 0.505 Sensitivity ContextFold: 0.657 CentroidFold: 0.441 Positive Predictive Value ContextFold: 0.744 CentroidFold: 0.579 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	357 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 CentroidFold: 0.575 Sensitivity CentroidAlifold(seed): 0.618 CentroidFold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.907 CentroidFold: 0.656 Number of pairs reference - predicted secondary structure: 357 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 CentroidFold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.468 CentroidFold: 0.518 Positive Predictive Value CentroidHomfold‑LAST: 0.870 CentroidFold: 0.636 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.741 CentroidFold: 0.617 Sensitivity TurboFold(20): 0.685 CentroidFold: 0.548 Positive Predictive Value TurboFold(20): 0.802 CentroidFold: 0.696 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.731 CentroidFold: 0.539 Sensitivity PETfold_pre2.0(20): 0.682 CentroidFold: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.785 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.736 CentroidFold: 0.601 Sensitivity PPfold(20): 0.641 CentroidFold: 0.531 Positive Predictive Value PPfold(20): 0.846 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs CentroidFold Matthews Correlation Coefficient Cylofold: 0.701 CentroidFold: 0.554 Sensitivity Cylofold: 0.673 CentroidFold: 0.497 Positive Predictive Value Cylofold: 0.734 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidFold: 0.539 Sensitivity CentroidAlifold(20): 0.597 CentroidFold: 0.474 Positive Predictive Value CentroidAlifold(20): 0.880 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.535 CentroidFold: 0.505 Sensitivity IPknot: 0.467 CentroidFold: 0.441 Positive Predictive Value IPknot: 0.613 CentroidFold: 0.579 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: 0.697 CentroidFold: 0.544 Sensitivity Pknots: 0.668 CentroidFold: 0.485 Positive Predictive Value Pknots: 0.733 CentroidFold: 0.621 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	362 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.630 CentroidFold: 0.575 Sensitivity MXScarna(seed): 0.534 CentroidFold: 0.505 Positive Predictive Value MXScarna(seed): 0.744 CentroidFold: 0.656 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.671 CentroidFold: 0.539 Sensitivity RNAalifold(20): 0.591 CentroidFold: 0.474 Positive Predictive Value RNAalifold(20): 0.762 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidFold: 0.631 Sensitivity RNASampler(seed): 0.572 CentroidFold: 0.554 Positive Predictive Value RNASampler(seed): 0.755 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.95070920198e-08	- Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.651 CentroidFold: 0.618 Sensitivity Multilign(20): 0.591 CentroidFold: 0.549 Positive Predictive Value Multilign(20): 0.718 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 CentroidFold: 0.570 Sensitivity RNAalifold(seed): 0.487 CentroidFold: 0.500 Positive Predictive Value RNAalifold(seed): 0.819 CentroidFold: 0.650 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.553 CentroidFold: 0.510 Sensitivity RNASampler(20): 0.434 CentroidFold: 0.445 Positive Predictive Value RNASampler(20): 0.705 CentroidFold: 0.585 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidFold: 0.539 Sensitivity MXScarna(20): 0.552 CentroidFold: 0.474 Positive Predictive Value MXScarna(20): 0.676 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.505 Contrafold: 0.491 Sensitivity CentroidFold: 0.441 Contrafold: 0.472 Positive Predictive Value CentroidFold: 0.579 Contrafold: 0.511 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.580 Murlet(20): 0.566 Sensitivity CentroidFold: 0.510 Murlet(20): 0.445 Positive Predictive Value CentroidFold: 0.661 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.505 Sfold: 0.453 Sensitivity CentroidFold: 0.441 Sfold: 0.402 Positive Predictive Value CentroidFold: 0.579 Sfold: 0.512 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.505 ProbKnot: 0.442 Sensitivity CentroidFold: 0.441 ProbKnot: 0.437 Positive Predictive Value CentroidFold: 0.579 ProbKnot: 0.447 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.505 MaxExpect: 0.446 Sensitivity CentroidFold: 0.441 MaxExpect: 0.433 Positive Predictive Value CentroidFold: 0.579 MaxExpect: 0.460 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.568 McQFold: 0.450 Sensitivity CentroidFold: 0.511 McQFold: 0.440 Positive Predictive Value CentroidFold: 0.632 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs CentroidFold Matthews Correlation Coefficient Murlet(seed): 0.584 CentroidFold: 0.528 Sensitivity Murlet(seed): 0.492 CentroidFold: 0.465 Positive Predictive Value Murlet(seed): 0.694 CentroidFold: 0.602 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.89431173416e-06	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.505 Fold: 0.416 Sensitivity CentroidFold: 0.441 Fold: 0.420 Positive Predictive Value CentroidFold: 0.579 Fold: 0.413 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.526 PknotsRG: 0.428 Sensitivity CentroidFold: 0.459 PknotsRG: 0.427 Positive Predictive Value CentroidFold: 0.603 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.505 UNAFold: 0.415 Sensitivity CentroidFold: 0.441 UNAFold: 0.413 Positive Predictive Value CentroidFold: 0.579 UNAFold: 0.418 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.633 CentroidFold: 0.627 Sensitivity TurboFold(seed): 0.562 CentroidFold: 0.567 Positive Predictive Value TurboFold(seed): 0.716 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000331720066723	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.574 RNAsubopt: 0.473 Sensitivity CentroidFold: 0.518 RNAsubopt: 0.480 Positive Predictive Value CentroidFold: 0.636 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.507 Afold: 0.413 Sensitivity CentroidFold: 0.439 Afold: 0.410 Positive Predictive Value CentroidFold: 0.586 Afold: 0.416 Number of pairs reference - predicted secondary structure: 564 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.565 RNASLOpt: 0.445 Sensitivity CentroidFold: 0.508 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.631 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.505 RNAfold: 0.407 Sensitivity CentroidFold: 0.441 RNAfold: 0.408 Positive Predictive Value CentroidFold: 0.579 RNAfold: 0.405 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.482 HotKnots: 0.453 Sensitivity CentroidFold: 0.430 HotKnots: 0.445 Positive Predictive Value CentroidFold: 0.548 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.544 RDfolder: 0.508 Sensitivity CentroidFold: 0.485 RDfolder: 0.432 Positive Predictive Value CentroidFold: 0.621 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.617 CMfinder(20): 0.482 Sensitivity CentroidFold: 0.548 CMfinder(20): 0.310 Positive Predictive Value CentroidFold: 0.696 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.569 RNAshapes: 0.408 Sensitivity CentroidFold: 0.513 RNAshapes: 0.404 Positive Predictive Value CentroidFold: 0.633 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.525 CRWrnafold: 0.395 Sensitivity CentroidFold: 0.459 CRWrnafold: 0.398 Positive Predictive Value CentroidFold: 0.600 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.539 Carnac(20): 0.496 Sensitivity CentroidFold: 0.474 Carnac(20): 0.277 Positive Predictive Value CentroidFold: 0.614 Carnac(20): 0.887 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.568 Vsfold5: 0.333 Sensitivity CentroidFold: 0.512 Vsfold5: 0.317 Positive Predictive Value CentroidFold: 0.631 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.568 Vsfold4: 0.337 Sensitivity CentroidFold: 0.512 Vsfold4: 0.310 Positive Predictive Value CentroidFold: 0.631 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.542 RNAwolf: 0.302 Sensitivity CentroidFold: 0.477 RNAwolf: 0.316 Positive Predictive Value CentroidFold: 0.616 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.599 CMfinder(seed): 0.363 Sensitivity CentroidFold: 0.525 CMfinder(seed): 0.184 Positive Predictive Value CentroidFold: 0.684 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.589 Carnac(seed): 0.253 Sensitivity CentroidFold: 0.540 Carnac(seed): 0.068 Positive Predictive Value CentroidFold: 0.643 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.539 RSpredict(20): 0.429 Sensitivity CentroidFold: 0.474 RSpredict(20): 0.348 Positive Predictive Value CentroidFold: 0.614 RSpredict(20): 0.530 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.544 Alterna: 0.393 Sensitivity CentroidFold: 0.485 Alterna: 0.365 Positive Predictive Value CentroidFold: 0.621 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.585 NanoFolder: 0.174 Sensitivity CentroidFold: 0.527 NanoFolder: 0.207 Positive Predictive Value CentroidFold: 0.652 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.576 RSpredict(seed): 0.368 Sensitivity CentroidFold: 0.506 RSpredict(seed): 0.224 Positive Predictive Value CentroidFold: 0.656 RSpredict(seed): 0.607 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.531 Mastr(20): 0.035 Sensitivity CentroidFold: 0.469 Mastr(20): 0.002 Positive Predictive Value CentroidFold: 0.601 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.614 Mastr(seed): 0.041 Sensitivity CentroidFold: 0.548 Mastr(seed): 0.002 Positive Predictive Value CentroidFold: 0.689 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.618 Multilign(seed): 0.575 Sensitivity CentroidFold: 0.514 Multilign(seed): 0.536 Positive Predictive Value CentroidFold: 0.750 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidFold: 0.618 Sensitivity PPfold(seed): 0.536 CentroidFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.486 MCFold: 0.290 Sensitivity CentroidFold: 0.436 MCFold: 0.320 Positive Predictive Value CentroidFold: 0.550 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	13 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 RNASampler(seed): 0.655 Sensitivity PETfold_pre2.0(seed): 0.572 RNASampler(seed): 0.572 Positive Predictive Value PETfold_pre2.0(seed): 0.769 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000309992208728	13 RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.655 ContextFold: 0.504 Sensitivity RNASampler(seed): 0.572 ContextFold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	13 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 RNASampler(seed): 0.655 Sensitivity CentroidAlifold(seed): 0.579 RNASampler(seed): 0.572 Positive Predictive Value CentroidAlifold(seed): 0.902 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.09700314043e-09	13 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidHomfold‑LAST: 0.583 Sensitivity RNASampler(seed): 0.572 CentroidHomfold‑LAST: 0.502 Positive Predictive Value RNASampler(seed): 0.755 CentroidHomfold‑LAST: 0.684 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.1398907247e-09	0 RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	11 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.831 RNASampler(seed): 0.646 Sensitivity Cylofold: 0.834 RNASampler(seed): 0.562 Positive Predictive Value Cylofold: 0.830 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.29209047668e-09	0 RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	13 RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.655 IPknot: 0.604 Sensitivity RNASampler(seed): 0.572 IPknot: 0.537 Positive Predictive Value RNASampler(seed): 0.755 IPknot: 0.686 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	12 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.803 RNASampler(seed): 0.641 Sensitivity Pknots: 0.820 RNASampler(seed): 0.562 Positive Predictive Value Pknots: 0.789 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.35333035499e-09	13 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 MXScarna(seed): 0.440 Sensitivity RNASampler(seed): 0.572 MXScarna(seed): 0.421 Positive Predictive Value RNASampler(seed): 0.755 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	0 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	13 RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidFold: 0.631 Sensitivity RNASampler(seed): 0.572 CentroidFold: 0.554 Positive Predictive Value RNASampler(seed): 0.755 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.95070920198e-08		? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(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) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAalifold(seed): 0.619 Sensitivity RNASampler(seed): 0.572 RNAalifold(seed): 0.477 Positive Predictive Value RNASampler(seed): 0.755 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.95070920198e-08	? RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.655 Contrafold: 0.582 Sensitivity RNASampler(seed): 0.572 Contrafold: 0.540 Positive Predictive Value RNASampler(seed): 0.755 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.655 Sfold: 0.475 Sensitivity RNASampler(seed): 0.572 Sfold: 0.442 Positive Predictive Value RNASampler(seed): 0.755 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.655 ProbKnot: 0.514 Sensitivity RNASampler(seed): 0.572 ProbKnot: 0.495 Positive Predictive Value RNASampler(seed): 0.755 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.655 MaxExpect: 0.513 Sensitivity RNASampler(seed): 0.572 MaxExpect: 0.488 Positive Predictive Value RNASampler(seed): 0.755 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	- McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.862 RNASampler(seed): 0.655 Sensitivity McQFold: 0.849 RNASampler(seed): 0.572 Positive Predictive Value McQFold: 0.877 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Murlet(seed): 0.482 Sensitivity RNASampler(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value RNASampler(seed): 0.755 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.655 Fold: 0.472 Sensitivity RNASampler(seed): 0.572 Fold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	- PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.819 RNASampler(seed): 0.655 Sensitivity PknotsRG: 0.818 RNASampler(seed): 0.572 Positive Predictive Value PknotsRG: 0.823 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.655 UNAFold: 0.481 Sensitivity RNASampler(seed): 0.572 UNAFold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.22797000563e-08	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.615 TurboFold(seed): 0.600 Sensitivity RNASampler(seed): 0.548 TurboFold(seed): 0.518 Positive Predictive Value RNASampler(seed): 0.697 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAsubopt: 0.463 Sensitivity RNASampler(seed): 0.572 RNAsubopt: 0.446 Positive Predictive Value RNASampler(seed): 0.755 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.642 Afold: 0.454 Sensitivity RNASampler(seed): 0.561 Afold: 0.427 Positive Predictive Value RNASampler(seed): 0.740 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNASLOpt: 0.584 Sensitivity RNASampler(seed): 0.572 RNASLOpt: 0.526 Positive Predictive Value RNASampler(seed): 0.755 RNASLOpt: 0.655 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.10032755566e-08	+ RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAfold: 0.476 Sensitivity RNASampler(seed): 0.572 RNAfold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.655 HotKnots: 0.522 Sensitivity RNASampler(seed): 0.572 HotKnots: 0.526 Positive Predictive Value RNASampler(seed): 0.755 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.641 RDfolder: 0.561 Sensitivity RNASampler(seed): 0.562 RDfolder: 0.481 Positive Predictive Value RNASampler(seed): 0.736 RDfolder: 0.663 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.84361416392e-08	? 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 RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAshapes: 0.447 Sensitivity RNASampler(seed): 0.572 RNAshapes: 0.432 Positive Predictive Value RNASampler(seed): 0.755 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.655 CRWrnafold: 0.446 Sensitivity RNASampler(seed): 0.572 CRWrnafold: 0.425 Positive Predictive Value RNASampler(seed): 0.755 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold5: 0.452 Sensitivity RNASampler(seed): 0.572 Vsfold5: 0.435 Positive Predictive Value RNASampler(seed): 0.755 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold4: 0.392 Sensitivity RNASampler(seed): 0.572 Vsfold4: 0.365 Positive Predictive Value RNASampler(seed): 0.755 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAwolf: 0.438 Sensitivity RNASampler(seed): 0.572 RNAwolf: 0.407 Positive Predictive Value RNASampler(seed): 0.755 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 CMfinder(seed): 0.443 Sensitivity RNASampler(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value RNASampler(seed): 0.753 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.26710183075e-09	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Carnac(seed): 0.582 Sensitivity RNASampler(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value RNASampler(seed): 0.755 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	? RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.641 Alterna: 0.384 Sensitivity RNASampler(seed): 0.562 Alterna: 0.365 Positive Predictive Value RNASampler(seed): 0.736 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	? NanoFolder vs RNASampler(seed) Matthews Correlation Coefficient NanoFolder: 0.585 RNASampler(seed): 0.559 Sensitivity NanoFolder: 0.654 RNASampler(seed): 0.481 Positive Predictive Value NanoFolder: 0.531 RNASampler(seed): 0.658 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RSpredict(seed): 0.488 Sensitivity RNASampler(seed): 0.572 RSpredict(seed): 0.425 Positive Predictive Value RNASampler(seed): 0.755 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	? Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Mastr(seed): 0.400 Sensitivity RNASampler(seed): 0.572 Mastr(seed): 0.242 Positive Predictive Value RNASampler(seed): 0.755 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.98760236454e-08	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RNASampler(seed): 0.569 Sensitivity Multilign(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value Multilign(seed): 0.625 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNASampler(seed): 0.569 Sensitivity PPfold(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value PPfold(seed): 0.833 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.621 MCFold: 0.354 Sensitivity RNASampler(seed): 0.546 MCFold: 0.415 Positive Predictive Value RNASampler(seed): 0.713 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08
Multilign(20)	196 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.753 Multilign(20): 0.651 Sensitivity PETfold_pre2.0(seed): 0.673 Multilign(20): 0.591 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.841 Multilign(20): 0.651 Sensitivity ContextFold: 0.793 Multilign(20): 0.591 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	156 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Multilign(20): 0.658 Sensitivity CentroidAlifold(seed): 0.546 Multilign(20): 0.595 Positive Predictive Value CentroidAlifold(seed): 0.953 Multilign(20): 0.730 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.701 Multilign(20): 0.651 Sensitivity CentroidHomfold‑LAST: 0.549 Multilign(20): 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.895 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Multilign(20): 0.651 Sensitivity TurboFold(20): 0.684 Multilign(20): 0.591 Positive Predictive Value TurboFold(20): 0.801 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Multilign(20): 0.651 Sensitivity PETfold_pre2.0(20): 0.653 Multilign(20): 0.591 Positive Predictive Value PETfold_pre2.0(20): 0.830 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	190 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.735 Multilign(20): 0.652 Sensitivity PPfold(20): 0.635 Multilign(20): 0.591 Positive Predictive Value PPfold(20): 0.852 Multilign(20): 0.719 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.862 Cylofold: 0.756 Sensitivity Multilign(20): 0.752 Cylofold: 0.677 Positive Predictive Value Multilign(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	196 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Multilign(20): 0.651 Sensitivity CentroidAlifold(20): 0.562 Multilign(20): 0.591 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.651 IPknot: 0.649 Sensitivity Multilign(20): 0.591 IPknot: 0.576 Positive Predictive Value Multilign(20): 0.718 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 0.231589081714	5 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.862 Pknots: 0.723 Sensitivity Multilign(20): 0.752 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	158 Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.659 MXScarna(seed): 0.655 Sensitivity Multilign(20): 0.595 MXScarna(seed): 0.540 Positive Predictive Value Multilign(20): 0.730 MXScarna(seed): 0.796 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 2.23046259944e-06	196 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Multilign(20): 0.651 Sensitivity RNAalifold(20): 0.532 Multilign(20): 0.591 Positive Predictive Value RNAalifold(20): 0.821 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.651 CentroidFold: 0.618 Sensitivity Multilign(20): 0.591 CentroidFold: 0.549 Positive Predictive Value Multilign(20): 0.718 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(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 RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RNAalifold(seed): 0.438 Sensitivity Multilign(20): 0.595 RNAalifold(seed): 0.242 Positive Predictive Value Multilign(20): 0.730 RNAalifold(seed): 0.793 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.610 RNASampler(20): 0.555 Sensitivity Multilign(20): 0.557 RNASampler(20): 0.436 Positive Predictive Value Multilign(20): 0.669 RNASampler(20): 0.708 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.651 MXScarna(20): 0.624 Sensitivity Multilign(20): 0.591 MXScarna(20): 0.548 Positive Predictive Value Multilign(20): 0.718 MXScarna(20): 0.711 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.651 Contrafold: 0.603 Sensitivity Multilign(20): 0.591 Contrafold: 0.577 Positive Predictive Value Multilign(20): 0.718 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.653 Murlet(20): 0.547 Sensitivity Multilign(20): 0.594 Murlet(20): 0.414 Positive Predictive Value Multilign(20): 0.719 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.651 Sfold: 0.567 Sensitivity Multilign(20): 0.591 Sfold: 0.502 Positive Predictive Value Multilign(20): 0.718 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.651 ProbKnot: 0.587 Sensitivity Multilign(20): 0.591 ProbKnot: 0.565 Positive Predictive Value Multilign(20): 0.718 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.651 MaxExpect: 0.588 Sensitivity Multilign(20): 0.591 MaxExpect: 0.562 Positive Predictive Value Multilign(20): 0.718 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.651 McQFold: 0.453 Sensitivity Multilign(20): 0.591 McQFold: 0.433 Positive Predictive Value Multilign(20): 0.718 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(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 Fold Matthews Correlation Coefficient Multilign(20): 0.651 Fold: 0.552 Sensitivity Multilign(20): 0.591 Fold: 0.543 Positive Predictive Value Multilign(20): 0.718 Fold: 0.563 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.651 PknotsRG: 0.510 Sensitivity Multilign(20): 0.591 PknotsRG: 0.501 Positive Predictive Value Multilign(20): 0.718 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.651 UNAFold: 0.533 Sensitivity Multilign(20): 0.591 UNAFold: 0.521 Positive Predictive Value Multilign(20): 0.718 UNAFold: 0.547 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(20): N/A Sensitivity TurboFold(seed): N/A Multilign(20): N/A Positive Predictive Value TurboFold(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 RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.651 RNAsubopt: 0.518 Sensitivity Multilign(20): 0.591 RNAsubopt: 0.516 Positive Predictive Value Multilign(20): 0.718 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.654 Afold: 0.545 Sensitivity Multilign(20): 0.592 Afold: 0.530 Positive Predictive Value Multilign(20): 0.724 Afold: 0.562 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.655 RNASLOpt: 0.456 Sensitivity Multilign(20): 0.597 RNASLOpt: 0.421 Positive Predictive Value Multilign(20): 0.719 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.651 RNAfold: 0.528 Sensitivity Multilign(20): 0.591 RNAfold: 0.519 Positive Predictive Value Multilign(20): 0.718 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.862 HotKnots: 0.717 Sensitivity Multilign(20): 0.752 HotKnots: 0.639 Positive Predictive Value Multilign(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.862 RDfolder: 0.664 Sensitivity Multilign(20): 0.752 RDfolder: 0.586 Positive Predictive Value Multilign(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.651 CMfinder(20): 0.484 Sensitivity Multilign(20): 0.591 CMfinder(20): 0.312 Positive Predictive Value Multilign(20): 0.718 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.651 RNAshapes: 0.454 Sensitivity Multilign(20): 0.592 RNAshapes: 0.440 Positive Predictive Value Multilign(20): 0.718 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.651 CRWrnafold: 0.453 Sensitivity Multilign(20): 0.591 CRWrnafold: 0.445 Positive Predictive Value Multilign(20): 0.718 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.651 Carnac(20): 0.351 Sensitivity Multilign(20): 0.591 Carnac(20): 0.144 Positive Predictive Value Multilign(20): 0.718 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.651 Vsfold5: 0.373 Sensitivity Multilign(20): 0.591 Vsfold5: 0.345 Positive Predictive Value Multilign(20): 0.717 Vsfold5: 0.405 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.649 Vsfold4: 0.395 Sensitivity Multilign(20): 0.590 Vsfold4: 0.357 Positive Predictive Value Multilign(20): 0.716 Vsfold4: 0.438 Number of pairs reference - predicted secondary structure: 192 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.651 RNAwolf: 0.366 Sensitivity Multilign(20): 0.591 RNAwolf: 0.376 Positive Predictive Value Multilign(20): 0.718 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-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	? Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.644 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.662 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.651 RSpredict(20): 0.335 Sensitivity Multilign(20): 0.591 RSpredict(20): 0.210 Positive Predictive Value Multilign(20): 0.718 RSpredict(20): 0.537 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.862 Alterna: 0.656 Sensitivity Multilign(20): 0.752 Alterna: 0.602 Positive Predictive Value Multilign(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.635 NanoFolder: 0.159 Sensitivity Multilign(20): 0.579 NanoFolder: 0.182 Positive Predictive Value Multilign(20): 0.699 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.659 RSpredict(seed): 0.066 Sensitivity Multilign(20): 0.595 RSpredict(seed): 0.017 Positive Predictive Value Multilign(20): 0.730 RSpredict(seed): 0.260 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.651 Mastr(20): 0.046 Sensitivity Multilign(20): 0.591 Mastr(20): 0.003 Positive Predictive Value Multilign(20): 0.718 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.661 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.599 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.731 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 142 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(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 MCFold Matthews Correlation Coefficient Multilign(20): 0.862 MCFold: 0.291 Sensitivity Multilign(20): 0.752 MCFold: 0.323 Positive Predictive Value Multilign(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
RNAalifold(seed)	363 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 RNAalifold(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.700 RNAalifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.820 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.804 RNAalifold(seed): 0.629 Sensitivity ContextFold: 0.759 RNAalifold(seed): 0.485 Positive Predictive Value ContextFold: 0.852 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 RNAalifold(seed): 0.636 Sensitivity CentroidAlifold(seed): 0.615 RNAalifold(seed): 0.490 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAalifold(seed): 0.827 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	291 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 RNAalifold(seed): 0.473 Sensitivity CentroidHomfold‑LAST: 0.508 RNAalifold(seed): 0.276 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 291 Wilcoxon single-rank test P-value: 3.56938820447e-08	166 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RNAalifold(seed): 0.448 Sensitivity TurboFold(20): 0.703 RNAalifold(seed): 0.252 Positive Predictive Value TurboFold(20): 0.824 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.765 RNAalifold(seed): 0.650 Sensitivity PETfold_pre2.0(20): 0.716 RNAalifold(seed): 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.817 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	165 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.751 RNAalifold(seed): 0.494 Sensitivity PPfold(20): 0.661 RNAalifold(seed): 0.307 Positive Predictive Value PPfold(20): 0.855 RNAalifold(seed): 0.796 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 RNAalifold(seed): 0.647 Sensitivity Cylofold: 0.772 RNAalifold(seed): 0.517 Positive Predictive Value Cylofold: 0.828 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.62913390836e-08	228 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.756 RNAalifold(seed): 0.650 Sensitivity CentroidAlifold(20): 0.634 RNAalifold(seed): 0.519 Positive Predictive Value CentroidAlifold(20): 0.901 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.629 IPknot: 0.604 Sensitivity RNAalifold(seed): 0.485 IPknot: 0.530 Positive Predictive Value RNAalifold(seed): 0.816 IPknot: 0.689 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.768 RNAalifold(seed): 0.651 Sensitivity Pknots: 0.748 RNAalifold(seed): 0.519 Positive Predictive Value Pknots: 0.792 RNAalifold(seed): 0.823 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.16131455263e-08	359 RNAalifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.636 MXScarna(seed): 0.628 Sensitivity RNAalifold(seed): 0.489 MXScarna(seed): 0.533 Positive Predictive Value RNAalifold(seed): 0.827 MXScarna(seed): 0.740 Number of pairs reference - predicted secondary structure: 359 Wilcoxon single-rank test P-value: 3.85233844192e-08	228 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.709 RNAalifold(seed): 0.650 Sensitivity RNAalifold(20): 0.626 RNAalifold(seed): 0.519 Positive Predictive Value RNAalifold(20): 0.803 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	362 RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.631 CentroidFold: 0.570 Sensitivity RNAalifold(seed): 0.487 CentroidFold: 0.500 Positive Predictive Value RNAalifold(seed): 0.819 CentroidFold: 0.650 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAalifold(seed): 0.619 Sensitivity RNASampler(seed): 0.572 RNAalifold(seed): 0.477 Positive Predictive Value RNASampler(seed): 0.755 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.95070920198e-08	156 Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RNAalifold(seed): 0.438 Sensitivity Multilign(20): 0.595 RNAalifold(seed): 0.242 Positive Predictive Value Multilign(20): 0.730 RNAalifold(seed): 0.793 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 RNAalifold(seed): 0.485 Sensitivity RNASampler(20): 0.384 RNAalifold(seed): 0.290 Positive Predictive Value RNASampler(20): 0.723 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNAalifold(seed) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 MXScarna(20): 0.642 Sensitivity RNAalifold(seed): 0.519 MXScarna(20): 0.575 Positive Predictive Value RNAalifold(seed): 0.814 MXScarna(20): 0.717 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Contrafold: 0.552 Sensitivity RNAalifold(seed): 0.485 Contrafold: 0.529 Positive Predictive Value RNAalifold(seed): 0.816 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.566 RNAalifold(seed): 0.541 Sensitivity Murlet(20): 0.437 RNAalifold(seed): 0.363 Positive Predictive Value Murlet(20): 0.734 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Sfold: 0.530 Sensitivity RNAalifold(seed): 0.485 Sfold: 0.469 Positive Predictive Value RNAalifold(seed): 0.816 Sfold: 0.600 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.629 ProbKnot: 0.503 Sensitivity RNAalifold(seed): 0.485 ProbKnot: 0.489 Positive Predictive Value RNAalifold(seed): 0.816 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.629 MaxExpect: 0.507 Sensitivity RNAalifold(seed): 0.485 MaxExpect: 0.489 Positive Predictive Value RNAalifold(seed): 0.816 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	- McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.484 RNAalifold(seed): 0.472 Sensitivity McQFold: 0.463 RNAalifold(seed): 0.275 Positive Predictive Value McQFold: 0.507 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.756 Murlet(seed): 0.584 Sensitivity RNAalifold(seed): 0.668 Murlet(seed): 0.492 Positive Predictive Value RNAalifold(seed): 0.856 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Fold: 0.475 Sensitivity RNAalifold(seed): 0.485 Fold: 0.472 Positive Predictive Value RNAalifold(seed): 0.816 Fold: 0.478 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.652 PknotsRG: 0.487 Sensitivity RNAalifold(seed): 0.496 PknotsRG: 0.479 Positive Predictive Value RNAalifold(seed): 0.856 PknotsRG: 0.496 Number of pairs reference - predicted secondary structure: 347 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.629 UNAFold: 0.491 Sensitivity RNAalifold(seed): 0.485 UNAFold: 0.482 Positive Predictive Value RNAalifold(seed): 0.816 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.638 TurboFold(seed): 0.633 Sensitivity RNAalifold(seed): 0.515 TurboFold(seed): 0.562 Positive Predictive Value RNAalifold(seed): 0.795 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00654937862799	- RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 RNAalifold(seed): 0.473 Sensitivity RNAsubopt: 0.530 RNAalifold(seed): 0.276 Positive Predictive Value RNAsubopt: 0.538 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 291 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.637 Afold: 0.478 Sensitivity RNAalifold(seed): 0.496 Afold: 0.470 Positive Predictive Value RNAalifold(seed): 0.817 Afold: 0.486 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs RNAalifold(seed) Matthews Correlation Coefficient RNASLOpt: 0.477 RNAalifold(seed): 0.470 Sensitivity RNASLOpt: 0.439 RNAalifold(seed): 0.273 Positive Predictive Value RNASLOpt: 0.520 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 246 Wilcoxon single-rank test P-value: 2.28033735003e-07	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.629 RNAfold: 0.472 Sensitivity RNAalifold(seed): 0.485 RNAfold: 0.466 Positive Predictive Value RNAalifold(seed): 0.816 RNAfold: 0.479 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.657 HotKnots: 0.603 Sensitivity RNAalifold(seed): 0.522 HotKnots: 0.588 Positive Predictive Value RNAalifold(seed): 0.833 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.651 RDfolder: 0.616 Sensitivity RNAalifold(seed): 0.519 RDfolder: 0.531 Positive Predictive Value RNAalifold(seed): 0.823 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.83464629825e-08	- CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.504 RNAalifold(seed): 0.448 Sensitivity CMfinder(20): 0.331 RNAalifold(seed): 0.252 Positive Predictive Value CMfinder(20): 0.771 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.486 RNAalifold(seed): 0.467 Sensitivity RNAshapes: 0.469 RNAalifold(seed): 0.270 Positive Predictive Value RNAshapes: 0.505 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.605 CRWrnafold: 0.476 Sensitivity RNAalifold(seed): 0.432 CRWrnafold: 0.468 Positive Predictive Value RNAalifold(seed): 0.850 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 324 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 Carnac(20): 0.509 Sensitivity RNAalifold(seed): 0.519 Carnac(20): 0.285 Positive Predictive Value RNAalifold(seed): 0.814 Carnac(20): 0.907 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.468 Vsfold5: 0.381 Sensitivity RNAalifold(seed): 0.271 Vsfold5: 0.351 Positive Predictive Value RNAalifold(seed): 0.809 Vsfold5: 0.416 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.470 Vsfold4: 0.407 Sensitivity RNAalifold(seed): 0.274 Vsfold4: 0.366 Positive Predictive Value RNAalifold(seed): 0.810 Vsfold4: 0.453 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNAwolf: 0.373 Sensitivity RNAalifold(seed): 0.275 RNAwolf: 0.382 Positive Predictive Value RNAalifold(seed): 0.812 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.450 CMfinder(seed): 0.363 Sensitivity RNAalifold(seed): 0.255 CMfinder(seed): 0.184 Positive Predictive Value RNAalifold(seed): 0.798 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Carnac(seed): 0.253 Sensitivity RNAalifold(seed): 0.465 Carnac(seed): 0.068 Positive Predictive Value RNAalifold(seed): 0.894 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 RSpredict(20): 0.480 Sensitivity RNAalifold(seed): 0.519 RSpredict(20): 0.380 Positive Predictive Value RNAalifold(seed): 0.814 RSpredict(20): 0.607 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.651 Alterna: 0.486 Sensitivity RNAalifold(seed): 0.519 Alterna: 0.455 Positive Predictive Value RNAalifold(seed): 0.823 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.457 NanoFolder: 0.184 Sensitivity RNAalifold(seed): 0.261 NanoFolder: 0.210 Positive Predictive Value RNAalifold(seed): 0.802 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.627 RSpredict(seed): 0.364 Sensitivity RNAalifold(seed): 0.477 RSpredict(seed): 0.222 Positive Predictive Value RNAalifold(seed): 0.826 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 352 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.444 Mastr(20): 0.048 Sensitivity RNAalifold(seed): 0.285 Mastr(20): 0.003 Positive Predictive Value RNAalifold(seed): 0.692 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.472 Mastr(seed): 0.041 Sensitivity RNAalifold(seed): 0.284 Mastr(seed): 0.002 Positive Predictive Value RNAalifold(seed): 0.785 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Multilign(seed): 0.575 Sensitivity RNAalifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value RNAalifold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNAalifold(seed): 0.644 Sensitivity PPfold(seed): 0.536 RNAalifold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 RNAalifold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.664 MCFold: 0.358 Sensitivity RNAalifold(seed): 0.537 MCFold: 0.409 Positive Predictive Value RNAalifold(seed): 0.828 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08
RNASampler(20)	50 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNASampler(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.592 RNASampler(20): 0.434 Positive Predictive Value PETfold_pre2.0(seed): 0.783 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.737 RNASampler(20): 0.553 Sensitivity ContextFold: 0.684 RNASampler(20): 0.434 Positive Predictive Value ContextFold: 0.795 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.702 RNASampler(20): 0.526 Sensitivity CentroidAlifold(seed): 0.526 RNASampler(20): 0.384 Positive Predictive Value CentroidAlifold(seed): 0.939 RNASampler(20): 0.723 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	50 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.682 RNASampler(20): 0.553 Sensitivity CentroidHomfold‑LAST: 0.537 RNASampler(20): 0.434 Positive Predictive Value CentroidHomfold‑LAST: 0.865 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.668 RNASampler(20): 0.553 Sensitivity TurboFold(20): 0.614 RNASampler(20): 0.434 Positive Predictive Value TurboFold(20): 0.727 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.656 RNASampler(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.575 RNASampler(20): 0.434 Positive Predictive Value PETfold_pre2.0(20): 0.749 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.661 RNASampler(20): 0.553 Sensitivity PPfold(20): 0.547 RNASampler(20): 0.434 Positive Predictive Value PPfold(20): 0.800 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.840 Cylofold: 0.756 Sensitivity RNASampler(20): 0.714 Cylofold: 0.677 Positive Predictive Value RNASampler(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	50 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.684 RNASampler(20): 0.553 Sensitivity CentroidAlifold(20): 0.546 RNASampler(20): 0.434 Positive Predictive Value CentroidAlifold(20): 0.857 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.589 RNASampler(20): 0.553 Sensitivity IPknot: 0.521 RNASampler(20): 0.434 Positive Predictive Value IPknot: 0.668 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.840 Pknots: 0.723 Sensitivity RNASampler(20): 0.714 Pknots: 0.632 Positive Predictive Value RNASampler(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	12 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.605 RNASampler(20): 0.526 Sensitivity MXScarna(seed): 0.485 RNASampler(20): 0.384 Positive Predictive Value MXScarna(seed): 0.757 RNASampler(20): 0.723 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	50 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.632 RNASampler(20): 0.553 Sensitivity RNAalifold(20): 0.526 RNASampler(20): 0.434 Positive Predictive Value RNAalifold(20): 0.760 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.553 CentroidFold: 0.510 Sensitivity RNASampler(20): 0.434 CentroidFold: 0.445 Positive Predictive Value RNASampler(20): 0.705 CentroidFold: 0.585 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	47 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.610 RNASampler(20): 0.555 Sensitivity Multilign(20): 0.557 RNASampler(20): 0.436 Positive Predictive Value Multilign(20): 0.669 RNASampler(20): 0.708 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 RNAalifold(seed): 0.485 Sensitivity RNASampler(20): 0.384 RNAalifold(seed): 0.290 Positive Predictive Value RNASampler(20): 0.723 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08		+ RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.553 MXScarna(20): 0.528 Sensitivity RNASampler(20): 0.434 MXScarna(20): 0.488 Positive Predictive Value RNASampler(20): 0.705 MXScarna(20): 0.572 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.553 Contrafold: 0.492 Sensitivity RNASampler(20): 0.434 Contrafold: 0.473 Positive Predictive Value RNASampler(20): 0.705 Contrafold: 0.514 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.580 RNASampler(20): 0.555 Sensitivity Murlet(20): 0.475 RNASampler(20): 0.438 Positive Predictive Value Murlet(20): 0.709 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.553 Sfold: 0.409 Sensitivity RNASampler(20): 0.434 Sfold: 0.353 Positive Predictive Value RNASampler(20): 0.705 Sfold: 0.476 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.553 ProbKnot: 0.469 Sensitivity RNASampler(20): 0.434 ProbKnot: 0.467 Positive Predictive Value RNASampler(20): 0.705 ProbKnot: 0.473 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.553 MaxExpect: 0.469 Sensitivity RNASampler(20): 0.434 MaxExpect: 0.455 Positive Predictive Value RNASampler(20): 0.705 MaxExpect: 0.484 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.553 McQFold: 0.398 Sensitivity RNASampler(20): 0.434 McQFold: 0.389 Positive Predictive Value RNASampler(20): 0.705 McQFold: 0.408 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): N/A Murlet(seed): N/A Sensitivity RNASampler(20): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.553 Fold: 0.462 Sensitivity RNASampler(20): 0.434 Fold: 0.463 Positive Predictive Value RNASampler(20): 0.705 Fold: 0.462 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.553 PknotsRG: 0.394 Sensitivity RNASampler(20): 0.434 PknotsRG: 0.399 Positive Predictive Value RNASampler(20): 0.705 PknotsRG: 0.391 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.553 UNAFold: 0.378 Sensitivity RNASampler(20): 0.434 UNAFold: 0.378 Positive Predictive Value RNASampler(20): 0.705 UNAFold: 0.379 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): N/A TurboFold(seed): N/A Sensitivity RNASampler(20): N/A TurboFold(seed): N/A Positive Predictive Value RNASampler(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.553 RNAsubopt: 0.369 Sensitivity RNASampler(20): 0.434 RNAsubopt: 0.377 Positive Predictive Value RNASampler(20): 0.705 RNAsubopt: 0.362 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.541 Afold: 0.489 Sensitivity RNASampler(20): 0.411 Afold: 0.481 Positive Predictive Value RNASampler(20): 0.715 Afold: 0.499 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.553 RNASLOpt: 0.386 Sensitivity RNASampler(20): 0.434 RNASLOpt: 0.366 Positive Predictive Value RNASampler(20): 0.705 RNASLOpt: 0.408 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.553 RNAfold: 0.398 Sensitivity RNASampler(20): 0.434 RNAfold: 0.404 Positive Predictive Value RNASampler(20): 0.705 RNAfold: 0.395 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.840 HotKnots: 0.717 Sensitivity RNASampler(20): 0.714 HotKnots: 0.639 Positive Predictive Value RNASampler(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.840 RDfolder: 0.664 Sensitivity RNASampler(20): 0.714 RDfolder: 0.586 Positive Predictive Value RNASampler(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.553 CMfinder(20): 0.386 Sensitivity RNASampler(20): 0.434 CMfinder(20): 0.232 Positive Predictive Value RNASampler(20): 0.705 CMfinder(20): 0.644 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.553 RNAshapes: 0.315 Sensitivity RNASampler(20): 0.433 RNAshapes: 0.313 Positive Predictive Value RNASampler(20): 0.707 RNAshapes: 0.318 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.553 CRWrnafold: 0.379 Sensitivity RNASampler(20): 0.434 CRWrnafold: 0.383 Positive Predictive Value RNASampler(20): 0.705 CRWrnafold: 0.377 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.553 Carnac(20): 0.468 Sensitivity RNASampler(20): 0.434 Carnac(20): 0.261 Positive Predictive Value RNASampler(20): 0.705 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.553 Vsfold5: 0.259 Sensitivity RNASampler(20): 0.434 Vsfold5: 0.248 Positive Predictive Value RNASampler(20): 0.705 Vsfold5: 0.272 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.553 Vsfold4: 0.260 Sensitivity RNASampler(20): 0.434 Vsfold4: 0.242 Positive Predictive Value RNASampler(20): 0.705 Vsfold4: 0.281 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.553 RNAwolf: 0.296 Sensitivity RNASampler(20): 0.434 RNAwolf: 0.315 Positive Predictive Value RNASampler(20): 0.705 RNAwolf: 0.281 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): N/A Carnac(seed): N/A Sensitivity RNASampler(20): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.553 RSpredict(20): 0.482 Sensitivity RNASampler(20): 0.434 RSpredict(20): 0.410 Positive Predictive Value RNASampler(20): 0.705 RSpredict(20): 0.569 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.840 Alterna: 0.656 Sensitivity RNASampler(20): 0.714 Alterna: 0.602 Positive Predictive Value RNASampler(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.634 NanoFolder: 0.100 Sensitivity RNASampler(20): 0.523 NanoFolder: 0.123 Positive Predictive Value RNASampler(20): 0.771 NanoFolder: 0.084 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 RSpredict(seed): 0.166 Sensitivity RNASampler(20): 0.384 RSpredict(seed): 0.052 Positive Predictive Value RNASampler(20): 0.723 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.553 Mastr(20): 0.096 Sensitivity RNASampler(20): 0.434 Mastr(20): 0.013 Positive Predictive Value RNASampler(20): 0.705 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.384 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.723 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): N/A PPfold(seed): N/A Sensitivity RNASampler(20): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.840 MCFold: 0.291 Sensitivity RNASampler(20): 0.714 MCFold: 0.323 Positive Predictive Value RNASampler(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
MXScarna(20)	286 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 MXScarna(20): 0.608 Sensitivity PETfold_pre2.0(seed): 0.709 MXScarna(20): 0.550 Positive Predictive Value PETfold_pre2.0(seed): 0.810 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.767 MXScarna(20): 0.608 Sensitivity ContextFold: 0.726 MXScarna(20): 0.550 Positive Predictive Value ContextFold: 0.811 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 MXScarna(20): 0.649 Sensitivity CentroidAlifold(seed): 0.647 MXScarna(20): 0.580 Positive Predictive Value CentroidAlifold(seed): 0.917 MXScarna(20): 0.727 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 MXScarna(20): 0.627 Sensitivity CentroidHomfold‑LAST: 0.552 MXScarna(20): 0.553 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(20): 0.713 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.741 MXScarna(20): 0.627 Sensitivity TurboFold(20): 0.685 MXScarna(20): 0.553 Positive Predictive Value TurboFold(20): 0.802 MXScarna(20): 0.713 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 MXScarna(20): 0.608 Sensitivity PETfold_pre2.0(20): 0.681 MXScarna(20): 0.550 Positive Predictive Value PETfold_pre2.0(20): 0.783 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.736 MXScarna(20): 0.628 Sensitivity PPfold(20): 0.641 MXScarna(20): 0.556 Positive Predictive Value PPfold(20): 0.846 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.837 Cylofold: 0.756 Sensitivity MXScarna(20): 0.752 Cylofold: 0.677 Positive Predictive Value MXScarna(20): 0.935 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	286 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 MXScarna(20): 0.608 Sensitivity CentroidAlifold(20): 0.595 MXScarna(20): 0.550 Positive Predictive Value CentroidAlifold(20): 0.879 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.608 IPknot: 0.577 Sensitivity MXScarna(20): 0.550 IPknot: 0.509 Positive Predictive Value MXScarna(20): 0.674 IPknot: 0.654 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.837 Pknots: 0.723 Sensitivity MXScarna(20): 0.752 Pknots: 0.632 Positive Predictive Value MXScarna(20): 0.935 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	226 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 MXScarna(20): 0.650 Sensitivity MXScarna(seed): 0.575 MXScarna(20): 0.581 Positive Predictive Value MXScarna(seed): 0.761 MXScarna(20): 0.727 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 MXScarna(20): 0.608 Sensitivity RNAalifold(20): 0.588 MXScarna(20): 0.550 Positive Predictive Value RNAalifold(20): 0.760 MXScarna(20): 0.674 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidFold: 0.539 Sensitivity MXScarna(20): 0.552 CentroidFold: 0.474 Positive Predictive Value MXScarna(20): 0.676 CentroidFold: 0.614 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	196 Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.651 MXScarna(20): 0.624 Sensitivity Multilign(20): 0.591 MXScarna(20): 0.548 Positive Predictive Value Multilign(20): 0.718 MXScarna(20): 0.711 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 RNAalifold(seed) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 MXScarna(20): 0.642 Sensitivity RNAalifold(seed): 0.519 MXScarna(20): 0.575 Positive Predictive Value RNAalifold(seed): 0.814 MXScarna(20): 0.717 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 4.83792096436e-08	50 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.553 MXScarna(20): 0.528 Sensitivity RNASampler(20): 0.434 MXScarna(20): 0.488 Positive Predictive Value RNASampler(20): 0.705 MXScarna(20): 0.572 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.608 Contrafold: 0.523 Sensitivity MXScarna(20): 0.550 Contrafold: 0.504 Positive Predictive Value MXScarna(20): 0.674 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.607 Murlet(20): 0.566 Sensitivity MXScarna(20): 0.542 Murlet(20): 0.445 Positive Predictive Value MXScarna(20): 0.681 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.608 Sfold: 0.496 Sensitivity MXScarna(20): 0.550 Sfold: 0.440 Positive Predictive Value MXScarna(20): 0.674 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.608 ProbKnot: 0.473 Sensitivity MXScarna(20): 0.550 ProbKnot: 0.463 Positive Predictive Value MXScarna(20): 0.674 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.608 MaxExpect: 0.478 Sensitivity MXScarna(20): 0.550 MaxExpect: 0.464 Positive Predictive Value MXScarna(20): 0.674 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.627 McQFold: 0.454 Sensitivity MXScarna(20): 0.553 McQFold: 0.434 Positive Predictive Value MXScarna(20): 0.713 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs MXScarna(20) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(20): N/A Sensitivity Murlet(seed): N/A MXScarna(20): N/A Positive Predictive Value Murlet(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 Fold Matthews Correlation Coefficient MXScarna(20): 0.608 Fold: 0.445 Sensitivity MXScarna(20): 0.550 Fold: 0.446 Positive Predictive Value MXScarna(20): 0.674 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.662 PknotsRG: 0.482 Sensitivity MXScarna(20): 0.593 PknotsRG: 0.474 Positive Predictive Value MXScarna(20): 0.739 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.608 UNAFold: 0.459 Sensitivity MXScarna(20): 0.550 UNAFold: 0.454 Positive Predictive Value MXScarna(20): 0.674 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): N/A MXScarna(20): N/A Sensitivity TurboFold(seed): N/A MXScarna(20): N/A Positive Predictive Value TurboFold(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 RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.627 RNAsubopt: 0.520 Sensitivity MXScarna(20): 0.553 RNAsubopt: 0.518 Positive Predictive Value MXScarna(20): 0.713 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.612 Afold: 0.453 Sensitivity MXScarna(20): 0.551 Afold: 0.449 Positive Predictive Value MXScarna(20): 0.680 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.620 RNASLOpt: 0.456 Sensitivity MXScarna(20): 0.547 RNASLOpt: 0.421 Positive Predictive Value MXScarna(20): 0.705 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.608 RNAfold: 0.444 Sensitivity MXScarna(20): 0.550 RNAfold: 0.443 Positive Predictive Value MXScarna(20): 0.674 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.837 HotKnots: 0.717 Sensitivity MXScarna(20): 0.752 HotKnots: 0.639 Positive Predictive Value MXScarna(20): 0.935 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.837 RDfolder: 0.664 Sensitivity MXScarna(20): 0.752 RDfolder: 0.586 Positive Predictive Value MXScarna(20): 0.935 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.627 CMfinder(20): 0.482 Sensitivity MXScarna(20): 0.553 CMfinder(20): 0.310 Positive Predictive Value MXScarna(20): 0.713 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.623 RNAshapes: 0.457 Sensitivity MXScarna(20): 0.548 RNAshapes: 0.442 Positive Predictive Value MXScarna(20): 0.709 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.650 CRWrnafold: 0.484 Sensitivity MXScarna(20): 0.579 CRWrnafold: 0.476 Positive Predictive Value MXScarna(20): 0.730 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.608 Carnac(20): 0.496 Sensitivity MXScarna(20): 0.550 Carnac(20): 0.277 Positive Predictive Value MXScarna(20): 0.674 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.623 Vsfold5: 0.371 Sensitivity MXScarna(20): 0.548 Vsfold5: 0.344 Positive Predictive Value MXScarna(20): 0.709 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.626 Vsfold4: 0.392 Sensitivity MXScarna(20): 0.552 Vsfold4: 0.355 Positive Predictive Value MXScarna(20): 0.712 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.627 RNAwolf: 0.368 Sensitivity MXScarna(20): 0.553 RNAwolf: 0.378 Positive Predictive Value MXScarna(20): 0.713 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-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 Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.776 Carnac(seed): 0.552 Sensitivity MXScarna(20): 0.752 Carnac(seed): 0.327 Positive Predictive Value MXScarna(20): 0.800 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.608 RSpredict(20): 0.425 Sensitivity MXScarna(20): 0.550 RSpredict(20): 0.345 Positive Predictive Value MXScarna(20): 0.674 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.837 Alterna: 0.656 Sensitivity MXScarna(20): 0.752 Alterna: 0.602 Positive Predictive Value MXScarna(20): 0.935 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.631 NanoFolder: 0.152 Sensitivity MXScarna(20): 0.556 NanoFolder: 0.174 Positive Predictive Value MXScarna(20): 0.718 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.648 RSpredict(seed): 0.402 Sensitivity MXScarna(20): 0.579 RSpredict(seed): 0.269 Positive Predictive Value MXScarna(20): 0.725 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.559 Mastr(20): 0.035 Sensitivity MXScarna(20): 0.503 Mastr(20): 0.002 Positive Predictive Value MXScarna(20): 0.621 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.644 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.562 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.740 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs MXScarna(20) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(20): N/A Sensitivity PPfold(seed): N/A MXScarna(20): N/A Positive Predictive Value PPfold(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 MCFold Matthews Correlation Coefficient MXScarna(20): 0.837 MCFold: 0.291 Sensitivity MXScarna(20): 0.752 MCFold: 0.323 Positive Predictive Value MXScarna(20): 0.935 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Contrafold	610 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Contrafold: 0.520 Sensitivity PETfold_pre2.0(seed): 0.651 Contrafold: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.676 Contrafold: 0.496 Sensitivity ContextFold: 0.634 Contrafold: 0.477 Positive Predictive Value ContextFold: 0.722 Contrafold: 0.515 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Contrafold: 0.558 Sensitivity CentroidAlifold(seed): 0.615 Contrafold: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.906 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Contrafold: 0.555 Sensitivity CentroidHomfold‑LAST: 0.468 Contrafold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Contrafold: 0.571 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.741 Contrafold: 0.602 Sensitivity TurboFold(20): 0.685 Contrafold: 0.577 Positive Predictive Value TurboFold(20): 0.802 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Contrafold: 0.523 Sensitivity PETfold_pre2.0(20): 0.681 Contrafold: 0.504 Positive Predictive Value PETfold_pre2.0(20): 0.783 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.736 Contrafold: 0.586 Sensitivity PPfold(20): 0.641 Contrafold: 0.561 Positive Predictive Value PPfold(20): 0.846 Contrafold: 0.612 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs Contrafold Matthews Correlation Coefficient Cylofold: 0.701 Contrafold: 0.528 Sensitivity Cylofold: 0.673 Contrafold: 0.491 Positive Predictive Value Cylofold: 0.734 Contrafold: 0.575 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Contrafold: 0.523 Sensitivity CentroidAlifold(20): 0.595 Contrafold: 0.504 Positive Predictive Value CentroidAlifold(20): 0.879 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.538 Contrafold: 0.497 Sensitivity IPknot: 0.470 Contrafold: 0.478 Positive Predictive Value IPknot: 0.616 Contrafold: 0.517 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Contrafold Matthews Correlation Coefficient Pknots: 0.697 Contrafold: 0.515 Sensitivity Pknots: 0.668 Contrafold: 0.477 Positive Predictive Value Pknots: 0.733 Contrafold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.628 Contrafold: 0.559 Sensitivity MXScarna(seed): 0.533 Contrafold: 0.535 Positive Predictive Value MXScarna(seed): 0.741 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.668 Contrafold: 0.523 Sensitivity RNAalifold(20): 0.588 Contrafold: 0.504 Positive Predictive Value RNAalifold(20): 0.760 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.505 Contrafold: 0.491 Sensitivity CentroidFold: 0.441 Contrafold: 0.472 Positive Predictive Value CentroidFold: 0.579 Contrafold: 0.511 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.655 Contrafold: 0.582 Sensitivity RNASampler(seed): 0.572 Contrafold: 0.540 Positive Predictive Value RNASampler(seed): 0.755 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	196 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.651 Contrafold: 0.603 Sensitivity Multilign(20): 0.591 Contrafold: 0.577 Positive Predictive Value Multilign(20): 0.718 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Contrafold: 0.552 Sensitivity RNAalifold(seed): 0.485 Contrafold: 0.529 Positive Predictive Value RNAalifold(seed): 0.816 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.553 Contrafold: 0.492 Sensitivity RNASampler(20): 0.434 Contrafold: 0.473 Positive Predictive Value RNASampler(20): 0.705 Contrafold: 0.514 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.608 Contrafold: 0.523 Sensitivity MXScarna(20): 0.550 Contrafold: 0.504 Positive Predictive Value MXScarna(20): 0.674 Contrafold: 0.543 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.566 Contrafold: 0.563 Sensitivity Murlet(20): 0.445 Contrafold: 0.540 Positive Predictive Value Murlet(20): 0.722 Contrafold: 0.588 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 0.000639955457467	+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.496 Sfold: 0.451 Sensitivity Contrafold: 0.477 Sfold: 0.400 Positive Predictive Value Contrafold: 0.515 Sfold: 0.509 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.496 ProbKnot: 0.442 Sensitivity Contrafold: 0.477 ProbKnot: 0.437 Positive Predictive Value Contrafold: 0.515 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.496 MaxExpect: 0.447 Sensitivity Contrafold: 0.477 MaxExpect: 0.435 Positive Predictive Value Contrafold: 0.515 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.550 McQFold: 0.450 Sensitivity Contrafold: 0.535 McQFold: 0.440 Positive Predictive Value Contrafold: 0.566 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Contrafold Matthews Correlation Coefficient Murlet(seed): 0.584 Contrafold: 0.507 Sensitivity Murlet(seed): 0.492 Contrafold: 0.477 Positive Predictive Value Murlet(seed): 0.694 Contrafold: 0.540 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.02549759314e-05	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.496 Fold: 0.417 Sensitivity Contrafold: 0.477 Fold: 0.421 Positive Predictive Value Contrafold: 0.515 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.512 PknotsRG: 0.428 Sensitivity Contrafold: 0.491 PknotsRG: 0.427 Positive Predictive Value Contrafold: 0.535 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.496 UNAFold: 0.414 Sensitivity Contrafold: 0.477 UNAFold: 0.412 Positive Predictive Value Contrafold: 0.515 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.633 Contrafold: 0.590 Sensitivity TurboFold(seed): 0.562 Contrafold: 0.558 Positive Predictive Value TurboFold(seed): 0.716 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.9460272886e-09	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.555 RNAsubopt: 0.473 Sensitivity Contrafold: 0.541 RNAsubopt: 0.480 Positive Predictive Value Contrafold: 0.571 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.494 Afold: 0.408 Sensitivity Contrafold: 0.472 Afold: 0.406 Positive Predictive Value Contrafold: 0.517 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.546 RNASLOpt: 0.445 Sensitivity Contrafold: 0.531 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.563 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.496 RNAfold: 0.407 Sensitivity Contrafold: 0.477 RNAfold: 0.408 Positive Predictive Value Contrafold: 0.515 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.458 HotKnots: 0.453 Sensitivity Contrafold: 0.435 HotKnots: 0.445 Positive Predictive Value Contrafold: 0.491 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0452037747897	= Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.515 RDfolder: 0.508 Sensitivity Contrafold: 0.477 RDfolder: 0.432 Positive Predictive Value Contrafold: 0.567 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0481694229406	+ Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.602 CMfinder(20): 0.482 Sensitivity Contrafold: 0.577 CMfinder(20): 0.310 Positive Predictive Value Contrafold: 0.630 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.550 RNAshapes: 0.408 Sensitivity Contrafold: 0.535 RNAshapes: 0.404 Positive Predictive Value Contrafold: 0.567 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.510 CRWrnafold: 0.395 Sensitivity Contrafold: 0.490 CRWrnafold: 0.398 Positive Predictive Value Contrafold: 0.532 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.523 Carnac(20): 0.496 Sensitivity Contrafold: 0.504 Carnac(20): 0.277 Positive Predictive Value Contrafold: 0.543 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.549 Vsfold5: 0.333 Sensitivity Contrafold: 0.535 Vsfold5: 0.317 Positive Predictive Value Contrafold: 0.565 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.549 Vsfold4: 0.337 Sensitivity Contrafold: 0.535 Vsfold4: 0.310 Positive Predictive Value Contrafold: 0.565 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.527 RNAwolf: 0.302 Sensitivity Contrafold: 0.506 RNAwolf: 0.316 Positive Predictive Value Contrafold: 0.549 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.577 CMfinder(seed): 0.363 Sensitivity Contrafold: 0.554 CMfinder(seed): 0.184 Positive Predictive Value Contrafold: 0.602 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.568 Carnac(seed): 0.253 Sensitivity Contrafold: 0.557 Carnac(seed): 0.068 Positive Predictive Value Contrafold: 0.579 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.523 RSpredict(20): 0.425 Sensitivity Contrafold: 0.504 RSpredict(20): 0.345 Positive Predictive Value Contrafold: 0.543 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.515 Alterna: 0.393 Sensitivity Contrafold: 0.477 Alterna: 0.365 Positive Predictive Value Contrafold: 0.567 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.565 NanoFolder: 0.174 Sensitivity Contrafold: 0.549 NanoFolder: 0.207 Positive Predictive Value Contrafold: 0.582 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.559 RSpredict(seed): 0.363 Sensitivity Contrafold: 0.534 RSpredict(seed): 0.222 Positive Predictive Value Contrafold: 0.585 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.513 Mastr(20): 0.035 Sensitivity Contrafold: 0.495 Mastr(20): 0.002 Positive Predictive Value Contrafold: 0.531 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.593 Mastr(seed): 0.040 Sensitivity Contrafold: 0.570 Mastr(seed): 0.002 Positive Predictive Value Contrafold: 0.618 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.596 Multilign(seed): 0.575 Sensitivity Contrafold: 0.521 Multilign(seed): 0.536 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.666 Contrafold: 0.596 Sensitivity PPfold(seed): 0.536 Contrafold: 0.521 Positive Predictive Value PPfold(seed): 0.833 Contrafold: 0.689 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.471 MCFold: 0.290 Sensitivity Contrafold: 0.440 MCFold: 0.320 Positive Predictive Value Contrafold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(20)	159 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.752 Murlet(20): 0.566 Sensitivity PETfold_pre2.0(seed): 0.683 Murlet(20): 0.445 Positive Predictive Value PETfold_pre2.0(seed): 0.828 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.805 Murlet(20): 0.566 Sensitivity ContextFold: 0.758 Murlet(20): 0.445 Positive Predictive Value ContextFold: 0.855 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.737 Murlet(20): 0.566 Sensitivity CentroidAlifold(seed): 0.583 Murlet(20): 0.437 Positive Predictive Value CentroidAlifold(seed): 0.933 Murlet(20): 0.734 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Murlet(20): 0.550 Sensitivity CentroidHomfold‑LAST: 0.547 Murlet(20): 0.416 Positive Predictive Value CentroidHomfold‑LAST: 0.888 Murlet(20): 0.727 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.730 Murlet(20): 0.550 Sensitivity TurboFold(20): 0.675 Murlet(20): 0.416 Positive Predictive Value TurboFold(20): 0.791 Murlet(20): 0.727 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.727 Murlet(20): 0.566 Sensitivity PETfold_pre2.0(20): 0.656 Murlet(20): 0.445 Positive Predictive Value PETfold_pre2.0(20): 0.805 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.726 Murlet(20): 0.554 Sensitivity PPfold(20): 0.627 Murlet(20): 0.420 Positive Predictive Value PPfold(20): 0.842 Murlet(20): 0.731 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: 0.756 Murlet(20): 0.741 Sensitivity Cylofold: 0.677 Murlet(20): 0.594 Positive Predictive Value Cylofold: 0.849 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	159 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.719 Murlet(20): 0.566 Sensitivity CentroidAlifold(20): 0.578 Murlet(20): 0.445 Positive Predictive Value CentroidAlifold(20): 0.894 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.622 Murlet(20): 0.566 Sensitivity IPknot: 0.548 Murlet(20): 0.445 Positive Predictive Value IPknot: 0.707 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.741 Pknots: 0.723 Sensitivity Murlet(20): 0.594 Pknots: 0.632 Positive Predictive Value Murlet(20): 0.929 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	118 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Murlet(20): 0.566 Sensitivity MXScarna(seed): 0.557 Murlet(20): 0.437 Positive Predictive Value MXScarna(seed): 0.770 Murlet(20): 0.734 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.666 Murlet(20): 0.566 Sensitivity RNAalifold(20): 0.560 Murlet(20): 0.445 Positive Predictive Value RNAalifold(20): 0.793 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.580 Murlet(20): 0.566 Sensitivity CentroidFold: 0.510 Murlet(20): 0.445 Positive Predictive Value CentroidFold: 0.661 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.85233844192e-08	0 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	138 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.653 Murlet(20): 0.547 Sensitivity Multilign(20): 0.594 Murlet(20): 0.414 Positive Predictive Value Multilign(20): 0.719 Murlet(20): 0.724 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.566 RNAalifold(seed): 0.541 Sensitivity Murlet(20): 0.437 RNAalifold(seed): 0.363 Positive Predictive Value Murlet(20): 0.734 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.580 RNASampler(20): 0.555 Sensitivity Murlet(20): 0.475 RNASampler(20): 0.438 Positive Predictive Value Murlet(20): 0.709 RNASampler(20): 0.705 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.607 Murlet(20): 0.566 Sensitivity MXScarna(20): 0.542 Murlet(20): 0.445 Positive Predictive Value MXScarna(20): 0.681 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.566 Contrafold: 0.563 Sensitivity Murlet(20): 0.445 Contrafold: 0.540 Positive Predictive Value Murlet(20): 0.722 Contrafold: 0.588 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 0.000639955457467		+ Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.566 Sfold: 0.531 Sensitivity Murlet(20): 0.445 Sfold: 0.465 Positive Predictive Value Murlet(20): 0.722 Sfold: 0.608 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.566 ProbKnot: 0.536 Sensitivity Murlet(20): 0.445 ProbKnot: 0.521 Positive Predictive Value Murlet(20): 0.722 ProbKnot: 0.552 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.566 MaxExpect: 0.537 Sensitivity Murlet(20): 0.445 MaxExpect: 0.517 Positive Predictive Value Murlet(20): 0.722 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.550 McQFold: 0.440 Sensitivity Murlet(20): 0.416 McQFold: 0.423 Positive Predictive Value Murlet(20): 0.727 McQFold: 0.460 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): N/A Murlet(seed): N/A Sensitivity Murlet(20): N/A Murlet(seed): N/A Positive Predictive Value Murlet(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.566 Fold: 0.506 Sensitivity Murlet(20): 0.445 Fold: 0.502 Positive Predictive Value Murlet(20): 0.722 Fold: 0.512 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.586 PknotsRG: 0.486 Sensitivity Murlet(20): 0.458 PknotsRG: 0.479 Positive Predictive Value Murlet(20): 0.751 PknotsRG: 0.494 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.566 UNAFold: 0.492 Sensitivity Murlet(20): 0.445 UNAFold: 0.484 Positive Predictive Value Murlet(20): 0.722 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.550 RNAsubopt: 0.501 Sensitivity Murlet(20): 0.416 RNAsubopt: 0.500 Positive Predictive Value Murlet(20): 0.727 RNAsubopt: 0.503 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.555 Afold: 0.501 Sensitivity Murlet(20): 0.432 Afold: 0.491 Positive Predictive Value Murlet(20): 0.715 Afold: 0.512 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.557 RNASLOpt: 0.438 Sensitivity Murlet(20): 0.426 RNASLOpt: 0.406 Positive Predictive Value Murlet(20): 0.730 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.566 RNAfold: 0.484 Sensitivity Murlet(20): 0.445 RNAfold: 0.480 Positive Predictive Value Murlet(20): 0.722 RNAfold: 0.490 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.741 HotKnots: 0.717 Sensitivity Murlet(20): 0.594 HotKnots: 0.639 Positive Predictive Value Murlet(20): 0.929 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.741 RDfolder: 0.664 Sensitivity Murlet(20): 0.594 RDfolder: 0.586 Positive Predictive Value Murlet(20): 0.929 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.550 CMfinder(20): 0.466 Sensitivity Murlet(20): 0.416 CMfinder(20): 0.296 Positive Predictive Value Murlet(20): 0.727 CMfinder(20): 0.733 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.555 RNAshapes: 0.433 Sensitivity Murlet(20): 0.421 RNAshapes: 0.420 Positive Predictive Value Murlet(20): 0.734 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.570 CRWrnafold: 0.445 Sensitivity Murlet(20): 0.440 CRWrnafold: 0.437 Positive Predictive Value Murlet(20): 0.741 CRWrnafold: 0.453 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.566 Carnac(20): 0.427 Sensitivity Murlet(20): 0.445 Carnac(20): 0.211 Positive Predictive Value Murlet(20): 0.722 Carnac(20): 0.866 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.555 Vsfold5: 0.354 Sensitivity Murlet(20): 0.422 Vsfold5: 0.329 Positive Predictive Value Murlet(20): 0.731 Vsfold5: 0.383 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.553 Vsfold4: 0.375 Sensitivity Murlet(20): 0.420 Vsfold4: 0.340 Positive Predictive Value Murlet(20): 0.730 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.550 RNAwolf: 0.355 Sensitivity Murlet(20): 0.416 RNAwolf: 0.367 Positive Predictive Value Murlet(20): 0.727 RNAwolf: 0.345 Number of pairs reference - predicted secondary structure: 150 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	? Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.333 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.243 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.456 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.566 RSpredict(20): 0.402 Sensitivity Murlet(20): 0.445 RSpredict(20): 0.292 Positive Predictive Value Murlet(20): 0.722 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.741 Alterna: 0.656 Sensitivity Murlet(20): 0.594 Alterna: 0.602 Positive Predictive Value Murlet(20): 0.929 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.541 NanoFolder: 0.151 Sensitivity Murlet(20): 0.405 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.725 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.560 RSpredict(seed): 0.224 Sensitivity Murlet(20): 0.430 RSpredict(seed): 0.104 Positive Predictive Value Murlet(20): 0.729 RSpredict(seed): 0.486 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.537 Mastr(20): 0.051 Sensitivity Murlet(20): 0.408 Mastr(20): 0.004 Positive Predictive Value Murlet(20): 0.708 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.540 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.396 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.738 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): N/A Murlet(20): N/A Sensitivity PPfold(seed): N/A Murlet(20): N/A Positive Predictive Value PPfold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.741 MCFold: 0.291 Sensitivity Murlet(20): 0.594 MCFold: 0.323 Positive Predictive Value Murlet(20): 0.929 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Sfold	610 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Sfold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.651 Sfold: 0.432 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Sfold: 0.544 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.676 Sfold: 0.451 Sensitivity ContextFold: 0.634 Sfold: 0.400 Positive Predictive Value ContextFold: 0.722 Sfold: 0.509 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Sfold: 0.535 Sensitivity CentroidAlifold(seed): 0.615 Sfold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.906 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Sfold: 0.516 Sensitivity CentroidHomfold‑LAST: 0.468 Sfold: 0.465 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Sfold: 0.574 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.741 Sfold: 0.569 Sensitivity TurboFold(20): 0.685 Sfold: 0.503 Positive Predictive Value TurboFold(20): 0.802 Sfold: 0.644 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Sfold: 0.496 Sensitivity PETfold_pre2.0(20): 0.681 Sfold: 0.440 Positive Predictive Value PETfold_pre2.0(20): 0.783 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.736 Sfold: 0.558 Sensitivity PPfold(20): 0.641 Sfold: 0.489 Positive Predictive Value PPfold(20): 0.846 Sfold: 0.637 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs Sfold Matthews Correlation Coefficient Cylofold: 0.701 Sfold: 0.516 Sensitivity Cylofold: 0.673 Sfold: 0.460 Positive Predictive Value Cylofold: 0.734 Sfold: 0.585 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Sfold: 0.496 Sensitivity CentroidAlifold(20): 0.595 Sfold: 0.440 Positive Predictive Value CentroidAlifold(20): 0.879 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.538 Sfold: 0.452 Sensitivity IPknot: 0.470 Sfold: 0.401 Positive Predictive Value IPknot: 0.616 Sfold: 0.510 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.697 Sfold: 0.482 Sensitivity Pknots: 0.668 Sfold: 0.435 Positive Predictive Value Pknots: 0.733 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.628 Sfold: 0.536 Sensitivity MXScarna(seed): 0.533 Sfold: 0.475 Positive Predictive Value MXScarna(seed): 0.741 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.668 Sfold: 0.496 Sensitivity RNAalifold(20): 0.588 Sfold: 0.440 Positive Predictive Value RNAalifold(20): 0.760 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.505 Sfold: 0.453 Sensitivity CentroidFold: 0.441 Sfold: 0.402 Positive Predictive Value CentroidFold: 0.579 Sfold: 0.512 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.655 Sfold: 0.475 Sensitivity RNASampler(seed): 0.572 Sfold: 0.442 Positive Predictive Value RNASampler(seed): 0.755 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	196 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.651 Sfold: 0.567 Sensitivity Multilign(20): 0.591 Sfold: 0.502 Positive Predictive Value Multilign(20): 0.718 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Sfold: 0.530 Sensitivity RNAalifold(seed): 0.485 Sfold: 0.469 Positive Predictive Value RNAalifold(seed): 0.816 Sfold: 0.600 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.553 Sfold: 0.409 Sensitivity RNASampler(20): 0.434 Sfold: 0.353 Positive Predictive Value RNASampler(20): 0.705 Sfold: 0.476 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.608 Sfold: 0.496 Sensitivity MXScarna(20): 0.550 Sfold: 0.440 Positive Predictive Value MXScarna(20): 0.674 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.496 Sfold: 0.451 Sensitivity Contrafold: 0.477 Sfold: 0.400 Positive Predictive Value Contrafold: 0.515 Sfold: 0.509 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.566 Sfold: 0.531 Sensitivity Murlet(20): 0.445 Sfold: 0.465 Positive Predictive Value Murlet(20): 0.722 Sfold: 0.608 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.451 ProbKnot: 0.442 Sensitivity Sfold: 0.400 ProbKnot: 0.437 Positive Predictive Value Sfold: 0.509 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.451 MaxExpect: 0.447 Sensitivity Sfold: 0.400 MaxExpect: 0.435 Positive Predictive Value Sfold: 0.509 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.510 McQFold: 0.450 Sensitivity Sfold: 0.459 McQFold: 0.440 Positive Predictive Value Sfold: 0.567 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): 0.584 Sfold: 0.414 Sensitivity Murlet(seed): 0.492 Sfold: 0.380 Positive Predictive Value Murlet(seed): 0.694 Sfold: 0.453 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.451 Fold: 0.417 Sensitivity Sfold: 0.400 Fold: 0.421 Positive Predictive Value Sfold: 0.509 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.473 PknotsRG: 0.428 Sensitivity Sfold: 0.420 PknotsRG: 0.427 Positive Predictive Value Sfold: 0.534 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.451 UNAFold: 0.414 Sensitivity Sfold: 0.400 UNAFold: 0.412 Positive Predictive Value Sfold: 0.509 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.633 Sfold: 0.512 Sensitivity TurboFold(seed): 0.562 Sfold: 0.489 Positive Predictive Value TurboFold(seed): 0.716 Sfold: 0.540 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.516 RNAsubopt: 0.473 Sensitivity Sfold: 0.465 RNAsubopt: 0.480 Positive Predictive Value Sfold: 0.574 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.454 Afold: 0.408 Sensitivity Sfold: 0.400 Afold: 0.406 Positive Predictive Value Sfold: 0.516 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.506 RNASLOpt: 0.445 Sensitivity Sfold: 0.455 RNASLOpt: 0.419 Positive Predictive Value Sfold: 0.565 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.451 RNAfold: 0.407 Sensitivity Sfold: 0.400 RNAfold: 0.408 Positive Predictive Value Sfold: 0.509 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.453 Sfold: 0.425 Sensitivity HotKnots: 0.445 Sfold: 0.377 Positive Predictive Value HotKnots: 0.469 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: 0.508 Sfold: 0.482 Sensitivity RDfolder: 0.432 Sfold: 0.435 Positive Predictive Value RDfolder: 0.609 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.09925167801e-06	+ Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.569 CMfinder(20): 0.482 Sensitivity Sfold: 0.503 CMfinder(20): 0.310 Positive Predictive Value Sfold: 0.644 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.511 RNAshapes: 0.408 Sensitivity Sfold: 0.460 RNAshapes: 0.404 Positive Predictive Value Sfold: 0.570 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.471 CRWrnafold: 0.395 Sensitivity Sfold: 0.417 CRWrnafold: 0.398 Positive Predictive Value Sfold: 0.533 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.496 Sfold: 0.496 Sensitivity Carnac(20): 0.277 Sfold: 0.440 Positive Predictive Value Carnac(20): 0.888 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 0.989275719324	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.510 Vsfold5: 0.333 Sensitivity Sfold: 0.459 Vsfold5: 0.317 Positive Predictive Value Sfold: 0.568 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.510 Vsfold4: 0.337 Sensitivity Sfold: 0.459 Vsfold4: 0.310 Positive Predictive Value Sfold: 0.568 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.484 RNAwolf: 0.302 Sensitivity Sfold: 0.430 RNAwolf: 0.316 Positive Predictive Value Sfold: 0.546 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.580 CMfinder(seed): 0.363 Sensitivity Sfold: 0.515 CMfinder(seed): 0.184 Positive Predictive Value Sfold: 0.653 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.564 Carnac(seed): 0.253 Sensitivity Sfold: 0.509 Carnac(seed): 0.068 Positive Predictive Value Sfold: 0.625 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.496 RSpredict(20): 0.425 Sensitivity Sfold: 0.440 RSpredict(20): 0.345 Positive Predictive Value Sfold: 0.559 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.482 Alterna: 0.393 Sensitivity Sfold: 0.435 Alterna: 0.365 Positive Predictive Value Sfold: 0.545 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.539 NanoFolder: 0.174 Sensitivity Sfold: 0.482 NanoFolder: 0.207 Positive Predictive Value Sfold: 0.604 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.535 RSpredict(seed): 0.363 Sensitivity Sfold: 0.474 RSpredict(seed): 0.222 Positive Predictive Value Sfold: 0.605 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.479 Mastr(20): 0.035 Sensitivity Sfold: 0.424 Mastr(20): 0.002 Positive Predictive Value Sfold: 0.540 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.572 Mastr(seed): 0.040 Sensitivity Sfold: 0.509 Mastr(seed): 0.002 Positive Predictive Value Sfold: 0.644 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.575 Sfold: 0.494 Sensitivity Multilign(seed): 0.536 Sfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.666 Sfold: 0.494 Sensitivity PPfold(seed): 0.536 Sfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.441 MCFold: 0.290 Sensitivity Sfold: 0.399 MCFold: 0.320 Positive Predictive Value Sfold: 0.497 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	610 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 ProbKnot: 0.472 Sensitivity PETfold_pre2.0(seed): 0.651 ProbKnot: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.790 ProbKnot: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.676 ProbKnot: 0.442 Sensitivity ContextFold: 0.634 ProbKnot: 0.437 Positive Predictive Value ContextFold: 0.722 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 ProbKnot: 0.509 Sensitivity CentroidAlifold(seed): 0.615 ProbKnot: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 ProbKnot: 0.524 Sensitivity CentroidHomfold‑LAST: 0.468 ProbKnot: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.870 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.741 ProbKnot: 0.587 Sensitivity TurboFold(20): 0.685 ProbKnot: 0.565 Positive Predictive Value TurboFold(20): 0.802 ProbKnot: 0.611 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 ProbKnot: 0.473 Sensitivity PETfold_pre2.0(20): 0.681 ProbKnot: 0.463 Positive Predictive Value PETfold_pre2.0(20): 0.783 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.736 ProbKnot: 0.563 Sensitivity PPfold(20): 0.641 ProbKnot: 0.543 Positive Predictive Value PPfold(20): 0.846 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.701 ProbKnot: 0.541 Sensitivity Cylofold: 0.673 ProbKnot: 0.512 Positive Predictive Value Cylofold: 0.734 ProbKnot: 0.579 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.723 ProbKnot: 0.473 Sensitivity CentroidAlifold(20): 0.595 ProbKnot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.879 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.538 ProbKnot: 0.443 Sensitivity IPknot: 0.470 ProbKnot: 0.438 Positive Predictive Value IPknot: 0.616 ProbKnot: 0.449 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.697 ProbKnot: 0.527 Sensitivity Pknots: 0.668 ProbKnot: 0.496 Positive Predictive Value Pknots: 0.733 ProbKnot: 0.570 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.628 ProbKnot: 0.510 Sensitivity MXScarna(seed): 0.533 ProbKnot: 0.495 Positive Predictive Value MXScarna(seed): 0.741 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.668 ProbKnot: 0.473 Sensitivity RNAalifold(20): 0.588 ProbKnot: 0.463 Positive Predictive Value RNAalifold(20): 0.760 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.505 ProbKnot: 0.442 Sensitivity CentroidFold: 0.441 ProbKnot: 0.437 Positive Predictive Value CentroidFold: 0.579 ProbKnot: 0.447 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.655 ProbKnot: 0.514 Sensitivity RNASampler(seed): 0.572 ProbKnot: 0.495 Positive Predictive Value RNASampler(seed): 0.755 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	196 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.651 ProbKnot: 0.587 Sensitivity Multilign(20): 0.591 ProbKnot: 0.565 Positive Predictive Value Multilign(20): 0.718 ProbKnot: 0.612 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.629 ProbKnot: 0.503 Sensitivity RNAalifold(seed): 0.485 ProbKnot: 0.489 Positive Predictive Value RNAalifold(seed): 0.816 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.553 ProbKnot: 0.469 Sensitivity RNASampler(20): 0.434 ProbKnot: 0.467 Positive Predictive Value RNASampler(20): 0.705 ProbKnot: 0.473 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.608 ProbKnot: 0.473 Sensitivity MXScarna(20): 0.550 ProbKnot: 0.463 Positive Predictive Value MXScarna(20): 0.674 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.496 ProbKnot: 0.442 Sensitivity Contrafold: 0.477 ProbKnot: 0.437 Positive Predictive Value Contrafold: 0.515 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.566 ProbKnot: 0.536 Sensitivity Murlet(20): 0.445 ProbKnot: 0.521 Positive Predictive Value Murlet(20): 0.722 ProbKnot: 0.552 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.451 ProbKnot: 0.442 Sensitivity Sfold: 0.400 ProbKnot: 0.437 Positive Predictive Value Sfold: 0.509 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08		- MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.447 ProbKnot: 0.442 Sensitivity MaxExpect: 0.435 ProbKnot: 0.437 Positive Predictive Value MaxExpect: 0.461 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.518 McQFold: 0.450 Sensitivity ProbKnot: 0.514 McQFold: 0.440 Positive Predictive Value ProbKnot: 0.524 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs ProbKnot Matthews Correlation Coefficient Murlet(seed): 0.584 ProbKnot: 0.427 Sensitivity Murlet(seed): 0.492 ProbKnot: 0.416 Positive Predictive Value Murlet(seed): 0.694 ProbKnot: 0.439 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 8.88051568979e-08	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.442 Fold: 0.417 Sensitivity ProbKnot: 0.437 Fold: 0.421 Positive Predictive Value ProbKnot: 0.448 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.463 PknotsRG: 0.428 Sensitivity ProbKnot: 0.456 PknotsRG: 0.427 Positive Predictive Value ProbKnot: 0.471 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.442 UNAFold: 0.414 Sensitivity ProbKnot: 0.437 UNAFold: 0.412 Positive Predictive Value ProbKnot: 0.448 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.633 ProbKnot: 0.558 Sensitivity TurboFold(seed): 0.562 ProbKnot: 0.554 Positive Predictive Value TurboFold(seed): 0.716 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.524 RNAsubopt: 0.473 Sensitivity ProbKnot: 0.519 RNAsubopt: 0.480 Positive Predictive Value ProbKnot: 0.532 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.437 Afold: 0.408 Sensitivity ProbKnot: 0.430 Afold: 0.406 Positive Predictive Value ProbKnot: 0.445 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.520 RNASLOpt: 0.445 Sensitivity ProbKnot: 0.514 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.528 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.442 RNAfold: 0.407 Sensitivity ProbKnot: 0.437 RNAfold: 0.408 Positive Predictive Value ProbKnot: 0.448 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.459 HotKnots: 0.453 Sensitivity ProbKnot: 0.440 HotKnots: 0.445 Positive Predictive Value ProbKnot: 0.487 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 6.29366556486e-06	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.527 RDfolder: 0.508 Sensitivity ProbKnot: 0.496 RDfolder: 0.432 Positive Predictive Value ProbKnot: 0.570 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.53079410487e-06	+ ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.587 CMfinder(20): 0.482 Sensitivity ProbKnot: 0.565 CMfinder(20): 0.310 Positive Predictive Value ProbKnot: 0.611 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.524 RNAshapes: 0.408 Sensitivity ProbKnot: 0.517 RNAshapes: 0.404 Positive Predictive Value ProbKnot: 0.532 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.464 CRWrnafold: 0.395 Sensitivity ProbKnot: 0.458 CRWrnafold: 0.398 Positive Predictive Value ProbKnot: 0.472 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.496 ProbKnot: 0.473 Sensitivity Carnac(20): 0.277 ProbKnot: 0.463 Positive Predictive Value Carnac(20): 0.888 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.522 Vsfold5: 0.333 Sensitivity ProbKnot: 0.516 Vsfold5: 0.317 Positive Predictive Value ProbKnot: 0.530 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.521 Vsfold4: 0.337 Sensitivity ProbKnot: 0.516 Vsfold4: 0.310 Positive Predictive Value ProbKnot: 0.528 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.488 RNAwolf: 0.302 Sensitivity ProbKnot: 0.482 RNAwolf: 0.316 Positive Predictive Value ProbKnot: 0.495 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.549 CMfinder(seed): 0.363 Sensitivity ProbKnot: 0.542 CMfinder(seed): 0.184 Positive Predictive Value ProbKnot: 0.557 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.529 Carnac(seed): 0.253 Sensitivity ProbKnot: 0.523 Carnac(seed): 0.068 Positive Predictive Value ProbKnot: 0.535 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.473 RSpredict(20): 0.425 Sensitivity ProbKnot: 0.463 RSpredict(20): 0.345 Positive Predictive Value ProbKnot: 0.483 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.527 Alterna: 0.393 Sensitivity ProbKnot: 0.496 Alterna: 0.365 Positive Predictive Value ProbKnot: 0.570 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.548 NanoFolder: 0.174 Sensitivity ProbKnot: 0.540 NanoFolder: 0.207 Positive Predictive Value ProbKnot: 0.558 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.512 RSpredict(seed): 0.363 Sensitivity ProbKnot: 0.498 RSpredict(seed): 0.222 Positive Predictive Value ProbKnot: 0.528 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.479 Mastr(20): 0.035 Sensitivity ProbKnot: 0.471 Mastr(20): 0.002 Positive Predictive Value ProbKnot: 0.487 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.574 Mastr(seed): 0.040 Sensitivity ProbKnot: 0.556 Mastr(seed): 0.002 Positive Predictive Value ProbKnot: 0.593 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.575 ProbKnot: 0.539 Sensitivity Multilign(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value Multilign(seed): 0.625 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.666 ProbKnot: 0.539 Sensitivity PPfold(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value PPfold(seed): 0.833 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.479 MCFold: 0.290 Sensitivity ProbKnot: 0.456 MCFold: 0.320 Positive Predictive Value ProbKnot: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	610 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 MaxExpect: 0.476 Sensitivity PETfold_pre2.0(seed): 0.651 MaxExpect: 0.463 Positive Predictive Value PETfold_pre2.0(seed): 0.790 MaxExpect: 0.489 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.676 MaxExpect: 0.447 Sensitivity ContextFold: 0.634 MaxExpect: 0.435 Positive Predictive Value ContextFold: 0.722 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 MaxExpect: 0.513 Sensitivity CentroidAlifold(seed): 0.615 MaxExpect: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.906 MaxExpect: 0.532 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 MaxExpect: 0.525 Sensitivity CentroidHomfold‑LAST: 0.468 MaxExpect: 0.511 Positive Predictive Value CentroidHomfold‑LAST: 0.870 MaxExpect: 0.541 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.741 MaxExpect: 0.588 Sensitivity TurboFold(20): 0.685 MaxExpect: 0.562 Positive Predictive Value TurboFold(20): 0.802 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 MaxExpect: 0.478 Sensitivity PETfold_pre2.0(20): 0.681 MaxExpect: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.783 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.736 MaxExpect: 0.564 Sensitivity PPfold(20): 0.641 MaxExpect: 0.540 Positive Predictive Value PPfold(20): 0.846 MaxExpect: 0.591 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.701 MaxExpect: 0.521 Sensitivity Cylofold: 0.673 MaxExpect: 0.483 Positive Predictive Value Cylofold: 0.734 MaxExpect: 0.570 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.723 MaxExpect: 0.478 Sensitivity CentroidAlifold(20): 0.595 MaxExpect: 0.464 Positive Predictive Value CentroidAlifold(20): 0.879 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.538 MaxExpect: 0.448 Sensitivity IPknot: 0.470 MaxExpect: 0.435 Positive Predictive Value IPknot: 0.616 MaxExpect: 0.462 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs MaxExpect Matthews Correlation Coefficient Pknots: 0.697 MaxExpect: 0.503 Sensitivity Pknots: 0.668 MaxExpect: 0.463 Positive Predictive Value Pknots: 0.733 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.628 MaxExpect: 0.513 Sensitivity MXScarna(seed): 0.533 MaxExpect: 0.495 Positive Predictive Value MXScarna(seed): 0.741 MaxExpect: 0.533 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.668 MaxExpect: 0.478 Sensitivity RNAalifold(20): 0.588 MaxExpect: 0.464 Positive Predictive Value RNAalifold(20): 0.760 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.505 MaxExpect: 0.446 Sensitivity CentroidFold: 0.441 MaxExpect: 0.433 Positive Predictive Value CentroidFold: 0.579 MaxExpect: 0.460 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.655 MaxExpect: 0.513 Sensitivity RNASampler(seed): 0.572 MaxExpect: 0.488 Positive Predictive Value RNASampler(seed): 0.755 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	196 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.651 MaxExpect: 0.588 Sensitivity Multilign(20): 0.591 MaxExpect: 0.562 Positive Predictive Value Multilign(20): 0.718 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.629 MaxExpect: 0.507 Sensitivity RNAalifold(seed): 0.485 MaxExpect: 0.489 Positive Predictive Value RNAalifold(seed): 0.816 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.553 MaxExpect: 0.469 Sensitivity RNASampler(20): 0.434 MaxExpect: 0.455 Positive Predictive Value RNASampler(20): 0.705 MaxExpect: 0.484 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.608 MaxExpect: 0.478 Sensitivity MXScarna(20): 0.550 MaxExpect: 0.464 Positive Predictive Value MXScarna(20): 0.674 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.496 MaxExpect: 0.447 Sensitivity Contrafold: 0.477 MaxExpect: 0.435 Positive Predictive Value Contrafold: 0.515 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.566 MaxExpect: 0.537 Sensitivity Murlet(20): 0.445 MaxExpect: 0.517 Positive Predictive Value Murlet(20): 0.722 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.451 MaxExpect: 0.447 Sensitivity Sfold: 0.400 MaxExpect: 0.435 Positive Predictive Value Sfold: 0.509 MaxExpect: 0.461 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.447 ProbKnot: 0.442 Sensitivity MaxExpect: 0.435 ProbKnot: 0.437 Positive Predictive Value MaxExpect: 0.461 ProbKnot: 0.448 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.520 McQFold: 0.450 Sensitivity MaxExpect: 0.506 McQFold: 0.440 Positive Predictive Value MaxExpect: 0.535 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs MaxExpect Matthews Correlation Coefficient Murlet(seed): 0.584 MaxExpect: 0.426 Sensitivity Murlet(seed): 0.492 MaxExpect: 0.408 Positive Predictive Value Murlet(seed): 0.694 MaxExpect: 0.446 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.05281399871e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.447 Fold: 0.417 Sensitivity MaxExpect: 0.435 Fold: 0.421 Positive Predictive Value MaxExpect: 0.461 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.467 PknotsRG: 0.428 Sensitivity MaxExpect: 0.451 PknotsRG: 0.427 Positive Predictive Value MaxExpect: 0.484 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.447 UNAFold: 0.414 Sensitivity MaxExpect: 0.435 UNAFold: 0.412 Positive Predictive Value MaxExpect: 0.461 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.633 MaxExpect: 0.563 Sensitivity TurboFold(seed): 0.562 MaxExpect: 0.549 Positive Predictive Value TurboFold(seed): 0.716 MaxExpect: 0.582 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.42028829171e-09	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.525 RNAsubopt: 0.473 Sensitivity MaxExpect: 0.511 RNAsubopt: 0.480 Positive Predictive Value MaxExpect: 0.541 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.443 Afold: 0.408 Sensitivity MaxExpect: 0.428 Afold: 0.406 Positive Predictive Value MaxExpect: 0.459 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.521 RNASLOpt: 0.445 Sensitivity MaxExpect: 0.506 RNASLOpt: 0.419 Positive Predictive Value MaxExpect: 0.538 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.447 RNAfold: 0.407 Sensitivity MaxExpect: 0.435 RNAfold: 0.408 Positive Predictive Value MaxExpect: 0.461 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.453 MaxExpect: 0.440 Sensitivity HotKnots: 0.445 MaxExpect: 0.414 Positive Predictive Value HotKnots: 0.469 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	= RDfolder vs MaxExpect Matthews Correlation Coefficient RDfolder: 0.508 MaxExpect: 0.503 Sensitivity RDfolder: 0.432 MaxExpect: 0.463 Positive Predictive Value RDfolder: 0.609 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0738256256282	+ MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.588 CMfinder(20): 0.482 Sensitivity MaxExpect: 0.562 CMfinder(20): 0.310 Positive Predictive Value MaxExpect: 0.617 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.524 RNAshapes: 0.408 Sensitivity MaxExpect: 0.509 RNAshapes: 0.404 Positive Predictive Value MaxExpect: 0.541 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.468 CRWrnafold: 0.395 Sensitivity MaxExpect: 0.452 CRWrnafold: 0.398 Positive Predictive Value MaxExpect: 0.485 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.496 MaxExpect: 0.478 Sensitivity Carnac(20): 0.277 MaxExpect: 0.464 Positive Predictive Value Carnac(20): 0.888 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.523 Vsfold5: 0.333 Sensitivity MaxExpect: 0.509 Vsfold5: 0.317 Positive Predictive Value MaxExpect: 0.539 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.522 Vsfold4: 0.337 Sensitivity MaxExpect: 0.508 Vsfold4: 0.310 Positive Predictive Value MaxExpect: 0.538 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.491 RNAwolf: 0.302 Sensitivity MaxExpect: 0.474 RNAwolf: 0.316 Positive Predictive Value MaxExpect: 0.510 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.552 CMfinder(seed): 0.363 Sensitivity MaxExpect: 0.535 CMfinder(seed): 0.184 Positive Predictive Value MaxExpect: 0.571 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.533 Carnac(seed): 0.253 Sensitivity MaxExpect: 0.524 Carnac(seed): 0.068 Positive Predictive Value MaxExpect: 0.543 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.478 RSpredict(20): 0.425 Sensitivity MaxExpect: 0.464 RSpredict(20): 0.345 Positive Predictive Value MaxExpect: 0.492 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.503 Alterna: 0.393 Sensitivity MaxExpect: 0.463 Alterna: 0.365 Positive Predictive Value MaxExpect: 0.559 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.549 NanoFolder: 0.174 Sensitivity MaxExpect: 0.532 NanoFolder: 0.207 Positive Predictive Value MaxExpect: 0.569 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.516 RSpredict(seed): 0.363 Sensitivity MaxExpect: 0.497 RSpredict(seed): 0.222 Positive Predictive Value MaxExpect: 0.535 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.483 Mastr(20): 0.035 Sensitivity MaxExpect: 0.469 Mastr(20): 0.002 Positive Predictive Value MaxExpect: 0.497 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.575 Mastr(seed): 0.040 Sensitivity MaxExpect: 0.552 Mastr(seed): 0.002 Positive Predictive Value MaxExpect: 0.600 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.575 MaxExpect: 0.553 Sensitivity Multilign(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value Multilign(seed): 0.625 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.666 MaxExpect: 0.553 Sensitivity PPfold(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value PPfold(seed): 0.833 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.457 MCFold: 0.290 Sensitivity MaxExpect: 0.424 MCFold: 0.320 Positive Predictive Value MaxExpect: 0.502 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	527 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 McQFold: 0.455 Sensitivity PETfold_pre2.0(seed): 0.590 McQFold: 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.787 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.712 McQFold: 0.450 Sensitivity ContextFold: 0.670 McQFold: 0.440 Positive Predictive Value ContextFold: 0.757 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	294 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 McQFold: 0.484 Sensitivity CentroidAlifold(seed): 0.522 McQFold: 0.463 Positive Predictive Value CentroidAlifold(seed): 0.919 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 294 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 McQFold: 0.459 Sensitivity CentroidHomfold‑LAST: 0.468 McQFold: 0.449 Positive Predictive Value CentroidHomfold‑LAST: 0.870 McQFold: 0.472 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.741 McQFold: 0.454 Sensitivity TurboFold(20): 0.685 McQFold: 0.434 Positive Predictive Value TurboFold(20): 0.802 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 McQFold: 0.454 Sensitivity PETfold_pre2.0(20): 0.653 McQFold: 0.434 Positive Predictive Value PETfold_pre2.0(20): 0.830 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.735 McQFold: 0.454 Sensitivity PPfold(20): 0.635 McQFold: 0.434 Positive Predictive Value PPfold(20): 0.851 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs McQFold Matthews Correlation Coefficient Cylofold: 0.701 McQFold: 0.676 Sensitivity Cylofold: 0.673 McQFold: 0.648 Positive Predictive Value Cylofold: 0.734 McQFold: 0.711 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 1.02208072244e-07	209 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.718 McQFold: 0.454 Sensitivity CentroidAlifold(20): 0.562 McQFold: 0.434 Positive Predictive Value CentroidAlifold(20): 0.917 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.597 McQFold: 0.450 Sensitivity IPknot: 0.539 McQFold: 0.440 Positive Predictive Value IPknot: 0.664 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.705 Pknots: 0.697 Sensitivity McQFold: 0.679 Pknots: 0.668 Positive Predictive Value McQFold: 0.738 Pknots: 0.733 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.68360786394e-05	299 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.594 McQFold: 0.486 Sensitivity MXScarna(seed): 0.475 McQFold: 0.465 Positive Predictive Value MXScarna(seed): 0.744 McQFold: 0.509 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.661 McQFold: 0.454 Sensitivity RNAalifold(20): 0.533 McQFold: 0.434 Positive Predictive Value RNAalifold(20): 0.820 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.568 McQFold: 0.450 Sensitivity CentroidFold: 0.511 McQFold: 0.440 Positive Predictive Value CentroidFold: 0.632 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.862 RNASampler(seed): 0.655 Sensitivity McQFold: 0.849 RNASampler(seed): 0.572 Positive Predictive Value McQFold: 0.877 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.24019667966e-08	196 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.651 McQFold: 0.453 Sensitivity Multilign(20): 0.591 McQFold: 0.433 Positive Predictive Value Multilign(20): 0.718 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.484 RNAalifold(seed): 0.472 Sensitivity McQFold: 0.463 RNAalifold(seed): 0.275 Positive Predictive Value McQFold: 0.507 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.553 McQFold: 0.398 Sensitivity RNASampler(20): 0.434 McQFold: 0.389 Positive Predictive Value RNASampler(20): 0.705 McQFold: 0.408 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.627 McQFold: 0.454 Sensitivity MXScarna(20): 0.553 McQFold: 0.434 Positive Predictive Value MXScarna(20): 0.713 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.550 McQFold: 0.450 Sensitivity Contrafold: 0.535 McQFold: 0.440 Positive Predictive Value Contrafold: 0.566 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.550 McQFold: 0.440 Sensitivity Murlet(20): 0.416 McQFold: 0.423 Positive Predictive Value Murlet(20): 0.727 McQFold: 0.460 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.510 McQFold: 0.450 Sensitivity Sfold: 0.459 McQFold: 0.440 Positive Predictive Value Sfold: 0.567 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.518 McQFold: 0.450 Sensitivity ProbKnot: 0.514 McQFold: 0.440 Positive Predictive Value ProbKnot: 0.524 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.520 McQFold: 0.450 Sensitivity MaxExpect: 0.506 McQFold: 0.440 Positive Predictive Value MaxExpect: 0.535 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.862 Murlet(seed): 0.482 Sensitivity McQFold: 0.849 Murlet(seed): 0.319 Positive Predictive Value McQFold: 0.877 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08	- Fold vs McQFold Matthews Correlation Coefficient Fold: 0.492 McQFold: 0.450 Sensitivity Fold: 0.494 McQFold: 0.440 Positive Predictive Value Fold: 0.491 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.475 McQFold: 0.450 Sensitivity PknotsRG: 0.477 McQFold: 0.440 Positive Predictive Value PknotsRG: 0.475 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	- UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.472 McQFold: 0.450 Sensitivity UNAFold: 0.470 McQFold: 0.440 Positive Predictive Value UNAFold: 0.476 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.807 TurboFold(seed): 0.633 Sensitivity McQFold: 0.803 TurboFold(seed): 0.562 Positive Predictive Value McQFold: 0.813 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.40200680498e-09	- RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.473 McQFold: 0.459 Sensitivity RNAsubopt: 0.480 McQFold: 0.449 Positive Predictive Value RNAsubopt: 0.468 McQFold: 0.472 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs McQFold Matthews Correlation Coefficient Afold: 0.486 McQFold: 0.457 Sensitivity Afold: 0.481 McQFold: 0.443 Positive Predictive Value Afold: 0.492 McQFold: 0.473 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.457 RNASLOpt: 0.445 Sensitivity McQFold: 0.446 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.470 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.471 McQFold: 0.450 Sensitivity RNAfold: 0.472 McQFold: 0.440 Positive Predictive Value RNAfold: 0.471 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs HotKnots Matthews Correlation Coefficient McQFold: 0.594 HotKnots: 0.453 Sensitivity McQFold: 0.583 HotKnots: 0.445 Positive Predictive Value McQFold: 0.611 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.508 Sensitivity McQFold: 0.679 RDfolder: 0.432 Positive Predictive Value McQFold: 0.738 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.482 McQFold: 0.454 Sensitivity CMfinder(20): 0.310 McQFold: 0.434 Positive Predictive Value CMfinder(20): 0.749 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.461 RNAshapes: 0.408 Sensitivity McQFold: 0.450 RNAshapes: 0.404 Positive Predictive Value McQFold: 0.475 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.450 CRWrnafold: 0.414 Sensitivity McQFold: 0.440 CRWrnafold: 0.417 Positive Predictive Value McQFold: 0.461 CRWrnafold: 0.412 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.454 Carnac(20): 0.365 Sensitivity McQFold: 0.434 Carnac(20): 0.155 Positive Predictive Value McQFold: 0.476 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.460 Vsfold5: 0.333 Sensitivity McQFold: 0.449 Vsfold5: 0.317 Positive Predictive Value McQFold: 0.473 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.459 Vsfold4: 0.337 Sensitivity McQFold: 0.448 Vsfold4: 0.310 Positive Predictive Value McQFold: 0.472 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.450 RNAwolf: 0.329 Sensitivity McQFold: 0.440 RNAwolf: 0.344 Positive Predictive Value McQFold: 0.461 RNAwolf: 0.317 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.526 CMfinder(seed): 0.363 Sensitivity McQFold: 0.510 CMfinder(seed): 0.184 Positive Predictive Value McQFold: 0.544 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.473 Carnac(seed): 0.141 Sensitivity McQFold: 0.465 Carnac(seed): 0.021 Positive Predictive Value McQFold: 0.482 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.454 RSpredict(20): 0.350 Sensitivity McQFold: 0.434 RSpredict(20): 0.222 Positive Predictive Value McQFold: 0.476 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.705 Alterna: 0.393 Sensitivity McQFold: 0.679 Alterna: 0.365 Positive Predictive Value McQFold: 0.738 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.448 NanoFolder: 0.174 Sensitivity McQFold: 0.436 NanoFolder: 0.207 Positive Predictive Value McQFold: 0.463 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.484 RSpredict(seed): 0.064 Sensitivity McQFold: 0.463 RSpredict(seed): 0.017 Positive Predictive Value McQFold: 0.508 RSpredict(seed): 0.248 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.454 Mastr(20): 0.044 Sensitivity McQFold: 0.434 Mastr(20): 0.003 Positive Predictive Value McQFold: 0.476 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.488 Mastr(seed): 0.041 Sensitivity McQFold: 0.468 Mastr(seed): 0.003 Positive Predictive Value McQFold: 0.510 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.932 Multilign(seed): 0.575 Sensitivity McQFold: 0.936 Multilign(seed): 0.536 Positive Predictive Value McQFold: 0.929 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.932 PPfold(seed): 0.666 Sensitivity McQFold: 0.936 PPfold(seed): 0.536 Positive Predictive Value McQFold: 0.929 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.652 MCFold: 0.290 Sensitivity McQFold: 0.631 MCFold: 0.320 Positive Predictive Value McQFold: 0.681 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	14 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.791 Murlet(seed): 0.584 Sensitivity PETfold_pre2.0(seed): 0.737 Murlet(seed): 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.849 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.26497248087e-08	14 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.697 Murlet(seed): 0.584 Sensitivity ContextFold: 0.636 Murlet(seed): 0.492 Positive Predictive Value ContextFold: 0.765 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.21563533328e-09	14 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Murlet(seed): 0.584 Sensitivity CentroidAlifold(seed): 0.718 Murlet(seed): 0.492 Positive Predictive Value CentroidAlifold(seed): 0.915 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	13 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Murlet(seed): 0.482 Sensitivity CentroidHomfold‑LAST: 0.502 Murlet(seed): 0.319 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.39162260866e-08	0 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): N/A Murlet(seed): N/A Sensitivity TurboFold(20): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(20): N/A Murlet(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 Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Murlet(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Murlet(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): N/A Murlet(seed): N/A Sensitivity PPfold(20): N/A Murlet(seed): N/A Positive Predictive Value PPfold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	11 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.831 Murlet(seed): 0.405 Sensitivity Cylofold: 0.834 Murlet(seed): 0.263 Positive Predictive Value Cylofold: 0.830 Murlet(seed): 0.633 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	0 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(20): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	14 Murlet(seed) vs IPknot Matthews Correlation Coefficient Murlet(seed): 0.584 IPknot: 0.543 Sensitivity Murlet(seed): 0.492 IPknot: 0.466 Positive Predictive Value Murlet(seed): 0.694 IPknot: 0.633 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.23236503487e-06	12 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.803 Murlet(seed): 0.432 Sensitivity Pknots: 0.820 Murlet(seed): 0.283 Positive Predictive Value Pknots: 0.789 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.59816551561e-08	14 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.614 Murlet(seed): 0.584 Sensitivity MXScarna(seed): 0.576 Murlet(seed): 0.492 Positive Predictive Value MXScarna(seed): 0.656 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10387130242e-07	0 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Murlet(seed): N/A Sensitivity RNAalifold(20): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	14 Murlet(seed) vs CentroidFold Matthews Correlation Coefficient Murlet(seed): 0.584 CentroidFold: 0.528 Sensitivity Murlet(seed): 0.492 CentroidFold: 0.465 Positive Predictive Value Murlet(seed): 0.694 CentroidFold: 0.602 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.89431173416e-06	13 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Murlet(seed): 0.482 Sensitivity RNASampler(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value RNASampler(seed): 0.755 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	0 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	14 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.756 Murlet(seed): 0.584 Sensitivity RNAalifold(seed): 0.668 Murlet(seed): 0.492 Positive Predictive Value RNAalifold(seed): 0.856 Murlet(seed): 0.694 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.52609899389e-08	0 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): N/A Murlet(seed): N/A Sensitivity RNASampler(20): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs MXScarna(20) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(20): N/A Sensitivity Murlet(seed): N/A MXScarna(20): N/A Positive Predictive Value Murlet(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	14 Murlet(seed) vs Contrafold Matthews Correlation Coefficient Murlet(seed): 0.584 Contrafold: 0.507 Sensitivity Murlet(seed): 0.492 Contrafold: 0.477 Positive Predictive Value Murlet(seed): 0.694 Contrafold: 0.540 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.02549759314e-05	0 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): N/A Murlet(seed): N/A Sensitivity Murlet(20): N/A Murlet(seed): N/A Positive Predictive Value Murlet(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	14 Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): 0.584 Sfold: 0.414 Sensitivity Murlet(seed): 0.492 Sfold: 0.380 Positive Predictive Value Murlet(seed): 0.694 Sfold: 0.453 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	14 Murlet(seed) vs ProbKnot Matthews Correlation Coefficient Murlet(seed): 0.584 ProbKnot: 0.427 Sensitivity Murlet(seed): 0.492 ProbKnot: 0.416 Positive Predictive Value Murlet(seed): 0.694 ProbKnot: 0.439 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 8.88051568979e-08	14 Murlet(seed) vs MaxExpect Matthews Correlation Coefficient Murlet(seed): 0.584 MaxExpect: 0.426 Sensitivity Murlet(seed): 0.492 MaxExpect: 0.408 Positive Predictive Value Murlet(seed): 0.694 MaxExpect: 0.446 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.05281399871e-08	13 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.862 Murlet(seed): 0.482 Sensitivity McQFold: 0.849 Murlet(seed): 0.319 Positive Predictive Value McQFold: 0.877 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08		+ Murlet(seed) vs Fold Matthews Correlation Coefficient Murlet(seed): 0.584 Fold: 0.412 Sensitivity Murlet(seed): 0.492 Fold: 0.399 Positive Predictive Value Murlet(seed): 0.694 Fold: 0.426 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ Murlet(seed) vs PknotsRG Matthews Correlation Coefficient Murlet(seed): 0.584 PknotsRG: 0.529 Sensitivity Murlet(seed): 0.492 PknotsRG: 0.526 Positive Predictive Value Murlet(seed): 0.694 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.13466906892e-05	+ Murlet(seed) vs UNAFold Matthews Correlation Coefficient Murlet(seed): 0.584 UNAFold: 0.402 Sensitivity Murlet(seed): 0.492 UNAFold: 0.392 Positive Predictive Value Murlet(seed): 0.694 UNAFold: 0.413 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.27752322258e-08	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Murlet(seed): 0.477 Sensitivity TurboFold(seed): 0.518 Murlet(seed): 0.333 Positive Predictive Value TurboFold(seed): 0.702 Murlet(seed): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): 0.482 RNAsubopt: 0.463 Sensitivity Murlet(seed): 0.319 RNAsubopt: 0.446 Positive Predictive Value Murlet(seed): 0.734 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.38571919282e-05	+ Murlet(seed) vs Afold Matthews Correlation Coefficient Murlet(seed): 0.588 Afold: 0.400 Sensitivity Murlet(seed): 0.501 Afold: 0.390 Positive Predictive Value Murlet(seed): 0.692 Afold: 0.412 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.70887622364e-08	- RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Murlet(seed): 0.482 Sensitivity RNASLOpt: 0.526 Murlet(seed): 0.319 Positive Predictive Value RNASLOpt: 0.655 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): 0.584 RNAfold: 0.414 Sensitivity Murlet(seed): 0.492 RNAfold: 0.405 Positive Predictive Value Murlet(seed): 0.694 RNAfold: 0.424 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	- HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.522 Murlet(seed): 0.482 Sensitivity HotKnots: 0.526 Murlet(seed): 0.319 Positive Predictive Value HotKnots: 0.524 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	- RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.561 Murlet(seed): 0.432 Sensitivity RDfolder: 0.481 Murlet(seed): 0.283 Positive Predictive Value RDfolder: 0.663 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.43573297697e-08	? Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.482 RNAshapes: 0.447 Sensitivity Murlet(seed): 0.319 RNAshapes: 0.432 Positive Predictive Value Murlet(seed): 0.734 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.74910108057e-08	+ Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.584 CRWrnafold: 0.403 Sensitivity Murlet(seed): 0.492 CRWrnafold: 0.388 Positive Predictive Value Murlet(seed): 0.694 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	? Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): N/A Murlet(seed): N/A Sensitivity Carnac(20): N/A Murlet(seed): N/A Positive Predictive Value Carnac(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold5: 0.452 Sensitivity Murlet(seed): 0.319 Vsfold5: 0.435 Positive Predictive Value Murlet(seed): 0.734 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.84361416392e-08	+ Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold4: 0.392 Sensitivity Murlet(seed): 0.319 Vsfold4: 0.365 Positive Predictive Value Murlet(seed): 0.734 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.482 RNAwolf: 0.438 Sensitivity Murlet(seed): 0.319 RNAwolf: 0.407 Positive Predictive Value Murlet(seed): 0.734 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.26434400251e-08	+ Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.488 CMfinder(seed): 0.443 Sensitivity Murlet(seed): 0.321 CMfinder(seed): 0.333 Positive Predictive Value Murlet(seed): 0.748 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.18293266588e-07	- Carnac(seed) vs Murlet(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Murlet(seed): 0.482 Sensitivity Carnac(seed): 0.354 Murlet(seed): 0.319 Positive Predictive Value Carnac(seed): 0.962 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.52299983238e-08	? RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): N/A Murlet(seed): N/A Sensitivity RSpredict(20): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs Alterna Matthews Correlation Coefficient Murlet(seed): 0.432 Alterna: 0.384 Sensitivity Murlet(seed): 0.283 Alterna: 0.365 Positive Predictive Value Murlet(seed): 0.667 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.2940533826e-08	? NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Murlet(seed): 0.574 Sensitivity NanoFolder: 0.654 Murlet(seed): 0.423 Positive Predictive Value NanoFolder: 0.531 Murlet(seed): 0.786 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.584 RSpredict(seed): 0.510 Sensitivity Murlet(seed): 0.492 RSpredict(seed): 0.414 Positive Predictive Value Murlet(seed): 0.694 RSpredict(seed): 0.627 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.2348692827e-08	? Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): N/A Murlet(seed): N/A Sensitivity Mastr(20): N/A Murlet(seed): N/A Positive Predictive Value Mastr(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 Mastr(seed): 0.400 Sensitivity Murlet(seed): 0.319 Mastr(seed): 0.242 Positive Predictive Value Murlet(seed): 0.734 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.47043379369e-08	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Murlet(seed): 0.518 Sensitivity Multilign(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value Multilign(seed): 0.625 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Murlet(seed): 0.518 Sensitivity PPfold(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value PPfold(seed): 0.833 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.456 MCFold: 0.354 Sensitivity Murlet(seed): 0.307 MCFold: 0.415 Positive Predictive Value Murlet(seed): 0.685 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08
Fold	610 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 Fold: 0.449 Sensitivity PETfold_pre2.0(seed): 0.651 Fold: 0.451 Positive Predictive Value PETfold_pre2.0(seed): 0.790 Fold: 0.447 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.676 Fold: 0.417 Sensitivity ContextFold: 0.634 Fold: 0.421 Positive Predictive Value ContextFold: 0.722 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 Fold: 0.480 Sensitivity CentroidAlifold(seed): 0.615 Fold: 0.477 Positive Predictive Value CentroidAlifold(seed): 0.906 Fold: 0.484 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 Fold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.468 Fold: 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Fold: 0.499 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.741 Fold: 0.551 Sensitivity TurboFold(20): 0.685 Fold: 0.542 Positive Predictive Value TurboFold(20): 0.802 Fold: 0.562 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Fold: 0.445 Sensitivity PETfold_pre2.0(20): 0.681 Fold: 0.446 Positive Predictive Value PETfold_pre2.0(20): 0.783 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.736 Fold: 0.529 Sensitivity PPfold(20): 0.641 Fold: 0.521 Positive Predictive Value PPfold(20): 0.846 Fold: 0.538 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.701 Fold: 0.528 Sensitivity Cylofold: 0.673 Fold: 0.491 Positive Predictive Value Cylofold: 0.734 Fold: 0.574 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Fold: 0.445 Sensitivity CentroidAlifold(20): 0.595 Fold: 0.446 Positive Predictive Value CentroidAlifold(20): 0.879 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.538 Fold: 0.418 Sensitivity IPknot: 0.470 Fold: 0.421 Positive Predictive Value IPknot: 0.616 Fold: 0.415 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.697 Fold: 0.504 Sensitivity Pknots: 0.668 Fold: 0.466 Positive Predictive Value Pknots: 0.733 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.628 Fold: 0.481 Sensitivity MXScarna(seed): 0.533 Fold: 0.478 Positive Predictive Value MXScarna(seed): 0.741 Fold: 0.485 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.668 Fold: 0.445 Sensitivity RNAalifold(20): 0.588 Fold: 0.446 Positive Predictive Value RNAalifold(20): 0.760 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.505 Fold: 0.416 Sensitivity CentroidFold: 0.441 Fold: 0.420 Positive Predictive Value CentroidFold: 0.579 Fold: 0.413 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.655 Fold: 0.472 Sensitivity RNASampler(seed): 0.572 Fold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	196 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.651 Fold: 0.552 Sensitivity Multilign(20): 0.591 Fold: 0.543 Positive Predictive Value Multilign(20): 0.718 Fold: 0.563 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.629 Fold: 0.475 Sensitivity RNAalifold(seed): 0.485 Fold: 0.472 Positive Predictive Value RNAalifold(seed): 0.816 Fold: 0.478 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.553 Fold: 0.462 Sensitivity RNASampler(20): 0.434 Fold: 0.463 Positive Predictive Value RNASampler(20): 0.705 Fold: 0.462 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.608 Fold: 0.445 Sensitivity MXScarna(20): 0.550 Fold: 0.446 Positive Predictive Value MXScarna(20): 0.674 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.496 Fold: 0.417 Sensitivity Contrafold: 0.477 Fold: 0.421 Positive Predictive Value Contrafold: 0.515 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.566 Fold: 0.506 Sensitivity Murlet(20): 0.445 Fold: 0.502 Positive Predictive Value Murlet(20): 0.722 Fold: 0.512 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.451 Fold: 0.417 Sensitivity Sfold: 0.400 Fold: 0.421 Positive Predictive Value Sfold: 0.509 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.442 Fold: 0.417 Sensitivity ProbKnot: 0.437 Fold: 0.421 Positive Predictive Value ProbKnot: 0.448 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.447 Fold: 0.417 Sensitivity MaxExpect: 0.435 Fold: 0.421 Positive Predictive Value MaxExpect: 0.461 Fold: 0.414 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.492 McQFold: 0.450 Sensitivity Fold: 0.494 McQFold: 0.440 Positive Predictive Value Fold: 0.491 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs Fold Matthews Correlation Coefficient Murlet(seed): 0.584 Fold: 0.412 Sensitivity Murlet(seed): 0.492 Fold: 0.399 Positive Predictive Value Murlet(seed): 0.694 Fold: 0.426 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08		+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.438 PknotsRG: 0.428 Sensitivity Fold: 0.439 PknotsRG: 0.427 Positive Predictive Value Fold: 0.437 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.417 UNAFold: 0.414 Sensitivity Fold: 0.421 UNAFold: 0.412 Positive Predictive Value Fold: 0.414 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.633 Fold: 0.510 Sensitivity TurboFold(seed): 0.562 Fold: 0.502 Positive Predictive Value TurboFold(seed): 0.716 Fold: 0.522 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.499 RNAsubopt: 0.473 Sensitivity Fold: 0.500 RNAsubopt: 0.480 Positive Predictive Value Fold: 0.499 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.413 Afold: 0.408 Sensitivity Fold: 0.415 Afold: 0.406 Positive Predictive Value Fold: 0.411 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.493 RNASLOpt: 0.445 Sensitivity Fold: 0.494 RNASLOpt: 0.419 Positive Predictive Value Fold: 0.494 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.417 RNAfold: 0.407 Sensitivity Fold: 0.421 RNAfold: 0.408 Positive Predictive Value Fold: 0.414 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.453 HotKnots: 0.453 Sensitivity Fold: 0.431 HotKnots: 0.445 Positive Predictive Value Fold: 0.485 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.236874878136	= RDfolder vs Fold Matthews Correlation Coefficient RDfolder: 0.508 Fold: 0.504 Sensitivity RDfolder: 0.432 Fold: 0.466 Positive Predictive Value RDfolder: 0.609 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0372146796483	+ Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.551 CMfinder(20): 0.482 Sensitivity Fold: 0.542 CMfinder(20): 0.310 Positive Predictive Value Fold: 0.562 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.497 RNAshapes: 0.408 Sensitivity Fold: 0.498 RNAshapes: 0.404 Positive Predictive Value Fold: 0.498 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.439 CRWrnafold: 0.395 Sensitivity Fold: 0.441 CRWrnafold: 0.398 Positive Predictive Value Fold: 0.439 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.496 Fold: 0.445 Sensitivity Carnac(20): 0.277 Fold: 0.446 Positive Predictive Value Carnac(20): 0.888 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.497 Vsfold5: 0.333 Sensitivity Fold: 0.498 Vsfold5: 0.317 Positive Predictive Value Fold: 0.497 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.495 Vsfold4: 0.337 Sensitivity Fold: 0.497 Vsfold4: 0.310 Positive Predictive Value Fold: 0.496 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.461 RNAwolf: 0.302 Sensitivity Fold: 0.462 RNAwolf: 0.316 Positive Predictive Value Fold: 0.461 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.505 CMfinder(seed): 0.363 Sensitivity Fold: 0.507 CMfinder(seed): 0.184 Positive Predictive Value Fold: 0.505 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.494 Carnac(seed): 0.253 Sensitivity Fold: 0.497 Carnac(seed): 0.068 Positive Predictive Value Fold: 0.491 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.445 RSpredict(20): 0.425 Sensitivity Fold: 0.446 RSpredict(20): 0.345 Positive Predictive Value Fold: 0.445 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.504 Alterna: 0.393 Sensitivity Fold: 0.466 Alterna: 0.365 Positive Predictive Value Fold: 0.556 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.511 NanoFolder: 0.174 Sensitivity Fold: 0.511 NanoFolder: 0.207 Positive Predictive Value Fold: 0.513 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.483 RSpredict(seed): 0.363 Sensitivity Fold: 0.479 RSpredict(seed): 0.222 Positive Predictive Value Fold: 0.487 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.451 Mastr(20): 0.035 Sensitivity Fold: 0.453 Mastr(20): 0.002 Positive Predictive Value Fold: 0.450 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.539 Mastr(seed): 0.040 Sensitivity Fold: 0.532 Mastr(seed): 0.002 Positive Predictive Value Fold: 0.548 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.575 Fold: 0.457 Sensitivity Multilign(seed): 0.536 Fold: 0.443 Positive Predictive Value Multilign(seed): 0.625 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.666 Fold: 0.457 Sensitivity PPfold(seed): 0.536 Fold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.472 MCFold: 0.290 Sensitivity Fold: 0.443 MCFold: 0.320 Positive Predictive Value Fold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	579 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.732 PknotsRG: 0.462 Sensitivity PETfold_pre2.0(seed): 0.659 PknotsRG: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.812 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.734 PknotsRG: 0.428 Sensitivity ContextFold: 0.689 PknotsRG: 0.427 Positive Predictive Value ContextFold: 0.783 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	346 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.763 PknotsRG: 0.488 Sensitivity CentroidAlifold(seed): 0.636 PknotsRG: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.915 PknotsRG: 0.497 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 PknotsRG: 0.479 Sensitivity CentroidHomfold‑LAST: 0.468 PknotsRG: 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.870 PknotsRG: 0.480 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.741 PknotsRG: 0.513 Sensitivity TurboFold(20): 0.685 PknotsRG: 0.504 Positive Predictive Value TurboFold(20): 0.802 PknotsRG: 0.524 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.785 PknotsRG: 0.482 Sensitivity PETfold_pre2.0(20): 0.732 PknotsRG: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.841 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	206 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.742 PknotsRG: 0.506 Sensitivity PPfold(20): 0.646 PknotsRG: 0.496 Positive Predictive Value PPfold(20): 0.854 PknotsRG: 0.517 Number of pairs reference - predicted secondary structure: 206 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.701 PknotsRG: 0.594 Sensitivity Cylofold: 0.673 PknotsRG: 0.572 Positive Predictive Value Cylofold: 0.734 PknotsRG: 0.623 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.782 PknotsRG: 0.482 Sensitivity CentroidAlifold(20): 0.667 PknotsRG: 0.474 Positive Predictive Value CentroidAlifold(20): 0.917 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.559 PknotsRG: 0.428 Sensitivity IPknot: 0.488 PknotsRG: 0.427 Positive Predictive Value IPknot: 0.642 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.697 PknotsRG: 0.627 Sensitivity Pknots: 0.668 PknotsRG: 0.601 Positive Predictive Value Pknots: 0.733 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	351 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.644 PknotsRG: 0.488 Sensitivity MXScarna(seed): 0.543 PknotsRG: 0.480 Positive Predictive Value MXScarna(seed): 0.766 PknotsRG: 0.497 Number of pairs reference - predicted secondary structure: 351 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.744 PknotsRG: 0.482 Sensitivity RNAalifold(20): 0.655 PknotsRG: 0.474 Positive Predictive Value RNAalifold(20): 0.846 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.526 PknotsRG: 0.428 Sensitivity CentroidFold: 0.459 PknotsRG: 0.427 Positive Predictive Value CentroidFold: 0.603 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.819 RNASampler(seed): 0.655 Sensitivity PknotsRG: 0.818 RNASampler(seed): 0.572 Positive Predictive Value PknotsRG: 0.823 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	196 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.651 PknotsRG: 0.510 Sensitivity Multilign(20): 0.591 PknotsRG: 0.501 Positive Predictive Value Multilign(20): 0.718 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	347 RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.652 PknotsRG: 0.487 Sensitivity RNAalifold(seed): 0.496 PknotsRG: 0.479 Positive Predictive Value RNAalifold(seed): 0.856 PknotsRG: 0.496 Number of pairs reference - predicted secondary structure: 347 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.553 PknotsRG: 0.394 Sensitivity RNASampler(20): 0.434 PknotsRG: 0.399 Positive Predictive Value RNASampler(20): 0.705 PknotsRG: 0.391 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.662 PknotsRG: 0.482 Sensitivity MXScarna(20): 0.593 PknotsRG: 0.474 Positive Predictive Value MXScarna(20): 0.739 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.512 PknotsRG: 0.428 Sensitivity Contrafold: 0.491 PknotsRG: 0.427 Positive Predictive Value Contrafold: 0.535 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	156 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.586 PknotsRG: 0.486 Sensitivity Murlet(20): 0.458 PknotsRG: 0.479 Positive Predictive Value Murlet(20): 0.751 PknotsRG: 0.494 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.473 PknotsRG: 0.428 Sensitivity Sfold: 0.420 PknotsRG: 0.427 Positive Predictive Value Sfold: 0.534 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.463 PknotsRG: 0.428 Sensitivity ProbKnot: 0.456 PknotsRG: 0.427 Positive Predictive Value ProbKnot: 0.471 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.467 PknotsRG: 0.428 Sensitivity MaxExpect: 0.451 PknotsRG: 0.427 Positive Predictive Value MaxExpect: 0.484 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.475 McQFold: 0.450 Sensitivity PknotsRG: 0.477 McQFold: 0.440 Positive Predictive Value PknotsRG: 0.475 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs PknotsRG Matthews Correlation Coefficient Murlet(seed): 0.584 PknotsRG: 0.529 Sensitivity Murlet(seed): 0.492 PknotsRG: 0.526 Positive Predictive Value Murlet(seed): 0.694 PknotsRG: 0.532 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.13466906892e-05	818 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.438 PknotsRG: 0.428 Sensitivity Fold: 0.439 PknotsRG: 0.427 Positive Predictive Value Fold: 0.437 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		- UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.435 PknotsRG: 0.428 Sensitivity UNAFold: 0.431 PknotsRG: 0.427 Positive Predictive Value UNAFold: 0.440 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.849 TurboFold(seed): 0.633 Sensitivity PknotsRG: 0.850 TurboFold(seed): 0.562 Positive Predictive Value PknotsRG: 0.850 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.00353292907e-09	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.479 RNAsubopt: 0.473 Sensitivity PknotsRG: 0.480 RNAsubopt: 0.480 Positive Predictive Value PknotsRG: 0.480 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.435 PknotsRG: 0.432 Sensitivity Afold: 0.429 PknotsRG: 0.428 Positive Predictive Value Afold: 0.441 PknotsRG: 0.437 Number of pairs reference - predicted secondary structure: 528 Wilcoxon single-rank test P-value: 1.47584956762e-07	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.468 RNASLOpt: 0.445 Sensitivity PknotsRG: 0.469 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.470 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.428 RNAfold: 0.425 Sensitivity PknotsRG: 0.427 RNAfold: 0.425 Positive Predictive Value PknotsRG: 0.429 RNAfold: 0.427 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.531 HotKnots: 0.453 Sensitivity PknotsRG: 0.525 HotKnots: 0.445 Positive Predictive Value PknotsRG: 0.544 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.627 RDfolder: 0.508 Sensitivity PknotsRG: 0.601 RDfolder: 0.432 Positive Predictive Value PknotsRG: 0.662 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.513 CMfinder(20): 0.482 Sensitivity PknotsRG: 0.504 CMfinder(20): 0.310 Positive Predictive Value PknotsRG: 0.524 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.476 RNAshapes: 0.408 Sensitivity PknotsRG: 0.476 RNAshapes: 0.404 Positive Predictive Value PknotsRG: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.427 CRWrnafold: 0.395 Sensitivity PknotsRG: 0.426 CRWrnafold: 0.398 Positive Predictive Value PknotsRG: 0.428 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.509 PknotsRG: 0.482 Sensitivity Carnac(20): 0.287 PknotsRG: 0.474 Positive Predictive Value Carnac(20): 0.904 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.474 Vsfold5: 0.333 Sensitivity PknotsRG: 0.475 Vsfold5: 0.317 Positive Predictive Value PknotsRG: 0.475 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.475 Vsfold4: 0.337 Sensitivity PknotsRG: 0.475 Vsfold4: 0.310 Positive Predictive Value PknotsRG: 0.476 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.446 RNAwolf: 0.302 Sensitivity PknotsRG: 0.445 RNAwolf: 0.316 Positive Predictive Value PknotsRG: 0.447 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.544 CMfinder(seed): 0.363 Sensitivity PknotsRG: 0.551 CMfinder(seed): 0.184 Positive Predictive Value PknotsRG: 0.539 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.529 Carnac(seed): 0.253 Sensitivity PknotsRG: 0.533 Carnac(seed): 0.068 Positive Predictive Value PknotsRG: 0.526 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.539 PknotsRG: 0.482 Sensitivity RSpredict(20): 0.421 PknotsRG: 0.474 Positive Predictive Value RSpredict(20): 0.690 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.627 Alterna: 0.393 Sensitivity PknotsRG: 0.601 Alterna: 0.365 Positive Predictive Value PknotsRG: 0.662 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.491 NanoFolder: 0.174 Sensitivity PknotsRG: 0.490 NanoFolder: 0.207 Positive Predictive Value PknotsRG: 0.493 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.493 RSpredict(seed): 0.398 Sensitivity PknotsRG: 0.485 RSpredict(seed): 0.233 Positive Predictive Value PknotsRG: 0.502 RSpredict(seed): 0.681 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.508 Mastr(20): 0.044 Sensitivity PknotsRG: 0.499 Mastr(20): 0.003 Positive Predictive Value PknotsRG: 0.519 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.527 Mastr(seed): 0.041 Sensitivity PknotsRG: 0.518 Mastr(seed): 0.003 Positive Predictive Value PknotsRG: 0.537 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.949 Multilign(seed): 0.575 Sensitivity PknotsRG: 0.943 Multilign(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 PPfold(seed): 0.666 Sensitivity PknotsRG: 0.943 PPfold(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.537 MCFold: 0.290 Sensitivity PknotsRG: 0.522 MCFold: 0.320 Positive Predictive Value PknotsRG: 0.560 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	610 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 UNAFold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.651 UNAFold: 0.445 Positive Predictive Value PETfold_pre2.0(seed): 0.790 UNAFold: 0.452 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	919 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.672 UNAFold: 0.414 Sensitivity ContextFold: 0.631 UNAFold: 0.412 Positive Predictive Value ContextFold: 0.716 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 919 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 UNAFold: 0.497 Sensitivity CentroidAlifold(seed): 0.615 UNAFold: 0.487 Positive Predictive Value CentroidAlifold(seed): 0.906 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 UNAFold: 0.478 Sensitivity CentroidHomfold‑LAST: 0.468 UNAFold: 0.474 Positive Predictive Value CentroidHomfold‑LAST: 0.870 UNAFold: 0.483 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.741 UNAFold: 0.532 Sensitivity TurboFold(20): 0.685 UNAFold: 0.520 Positive Predictive Value TurboFold(20): 0.802 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 UNAFold: 0.459 Sensitivity PETfold_pre2.0(20): 0.681 UNAFold: 0.454 Positive Predictive Value PETfold_pre2.0(20): 0.783 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.736 UNAFold: 0.520 Sensitivity PPfold(20): 0.641 UNAFold: 0.508 Positive Predictive Value PPfold(20): 0.846 UNAFold: 0.534 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.701 UNAFold: 0.474 Sensitivity Cylofold: 0.673 UNAFold: 0.438 Positive Predictive Value Cylofold: 0.734 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 UNAFold: 0.459 Sensitivity CentroidAlifold(20): 0.595 UNAFold: 0.454 Positive Predictive Value CentroidAlifold(20): 0.879 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.538 UNAFold: 0.415 Sensitivity IPknot: 0.470 UNAFold: 0.412 Positive Predictive Value IPknot: 0.616 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.697 UNAFold: 0.468 Sensitivity Pknots: 0.668 UNAFold: 0.431 Positive Predictive Value Pknots: 0.733 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.628 UNAFold: 0.497 Sensitivity MXScarna(seed): 0.533 UNAFold: 0.487 Positive Predictive Value MXScarna(seed): 0.741 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.668 UNAFold: 0.459 Sensitivity RNAalifold(20): 0.588 UNAFold: 0.454 Positive Predictive Value RNAalifold(20): 0.760 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.505 UNAFold: 0.415 Sensitivity CentroidFold: 0.441 UNAFold: 0.413 Positive Predictive Value CentroidFold: 0.579 UNAFold: 0.418 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.655 UNAFold: 0.481 Sensitivity RNASampler(seed): 0.572 UNAFold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.22797000563e-08	196 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.651 UNAFold: 0.533 Sensitivity Multilign(20): 0.591 UNAFold: 0.521 Positive Predictive Value Multilign(20): 0.718 UNAFold: 0.547 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.629 UNAFold: 0.491 Sensitivity RNAalifold(seed): 0.485 UNAFold: 0.482 Positive Predictive Value RNAalifold(seed): 0.816 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.553 UNAFold: 0.378 Sensitivity RNASampler(20): 0.434 UNAFold: 0.378 Positive Predictive Value RNASampler(20): 0.705 UNAFold: 0.379 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.608 UNAFold: 0.459 Sensitivity MXScarna(20): 0.550 UNAFold: 0.454 Positive Predictive Value MXScarna(20): 0.674 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.496 UNAFold: 0.414 Sensitivity Contrafold: 0.477 UNAFold: 0.412 Positive Predictive Value Contrafold: 0.515 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.566 UNAFold: 0.492 Sensitivity Murlet(20): 0.445 UNAFold: 0.484 Positive Predictive Value Murlet(20): 0.722 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.451 UNAFold: 0.414 Sensitivity Sfold: 0.400 UNAFold: 0.412 Positive Predictive Value Sfold: 0.509 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.442 UNAFold: 0.414 Sensitivity ProbKnot: 0.437 UNAFold: 0.412 Positive Predictive Value ProbKnot: 0.448 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.447 UNAFold: 0.414 Sensitivity MaxExpect: 0.435 UNAFold: 0.412 Positive Predictive Value MaxExpect: 0.461 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.472 McQFold: 0.450 Sensitivity UNAFold: 0.470 McQFold: 0.440 Positive Predictive Value UNAFold: 0.476 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs UNAFold Matthews Correlation Coefficient Murlet(seed): 0.584 UNAFold: 0.402 Sensitivity Murlet(seed): 0.492 UNAFold: 0.392 Positive Predictive Value Murlet(seed): 0.694 UNAFold: 0.413 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.27752322258e-08	910 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.417 UNAFold: 0.414 Sensitivity Fold: 0.421 UNAFold: 0.412 Positive Predictive Value Fold: 0.414 UNAFold: 0.417 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.435 PknotsRG: 0.428 Sensitivity UNAFold: 0.431 PknotsRG: 0.427 Positive Predictive Value UNAFold: 0.440 PknotsRG: 0.429 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		- TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.633 UNAFold: 0.510 Sensitivity TurboFold(seed): 0.562 UNAFold: 0.494 Positive Predictive Value TurboFold(seed): 0.716 UNAFold: 0.532 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.478 RNAsubopt: 0.473 Sensitivity UNAFold: 0.474 RNAsubopt: 0.480 Positive Predictive Value UNAFold: 0.483 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.416 Afold: 0.408 Sensitivity UNAFold: 0.412 Afold: 0.406 Positive Predictive Value UNAFold: 0.421 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.468 RNASLOpt: 0.445 Sensitivity UNAFold: 0.464 RNASLOpt: 0.419 Positive Predictive Value UNAFold: 0.474 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.414 RNAfold: 0.407 Sensitivity UNAFold: 0.412 RNAfold: 0.408 Positive Predictive Value UNAFold: 0.417 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.453 UNAFold: 0.412 Sensitivity HotKnots: 0.445 UNAFold: 0.390 Positive Predictive Value HotKnots: 0.469 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs UNAFold Matthews Correlation Coefficient RDfolder: 0.508 UNAFold: 0.468 Sensitivity RDfolder: 0.432 UNAFold: 0.431 Positive Predictive Value RDfolder: 0.609 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.532 CMfinder(20): 0.482 Sensitivity UNAFold: 0.520 CMfinder(20): 0.310 Positive Predictive Value UNAFold: 0.546 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.474 RNAshapes: 0.408 Sensitivity UNAFold: 0.470 RNAshapes: 0.404 Positive Predictive Value UNAFold: 0.480 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.433 CRWrnafold: 0.395 Sensitivity UNAFold: 0.429 CRWrnafold: 0.398 Positive Predictive Value UNAFold: 0.438 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.496 UNAFold: 0.459 Sensitivity Carnac(20): 0.277 UNAFold: 0.454 Positive Predictive Value Carnac(20): 0.888 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.473 Vsfold5: 0.333 Sensitivity UNAFold: 0.469 Vsfold5: 0.317 Positive Predictive Value UNAFold: 0.478 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.473 Vsfold4: 0.337 Sensitivity UNAFold: 0.469 Vsfold4: 0.310 Positive Predictive Value UNAFold: 0.478 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.445 RNAwolf: 0.302 Sensitivity UNAFold: 0.440 RNAwolf: 0.316 Positive Predictive Value UNAFold: 0.450 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.485 CMfinder(seed): 0.363 Sensitivity UNAFold: 0.476 CMfinder(seed): 0.184 Positive Predictive Value UNAFold: 0.495 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.511 Carnac(seed): 0.253 Sensitivity UNAFold: 0.508 Carnac(seed): 0.068 Positive Predictive Value UNAFold: 0.514 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.459 RSpredict(20): 0.425 Sensitivity UNAFold: 0.454 RSpredict(20): 0.345 Positive Predictive Value UNAFold: 0.465 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.468 Alterna: 0.393 Sensitivity UNAFold: 0.431 Alterna: 0.365 Positive Predictive Value UNAFold: 0.521 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.498 NanoFolder: 0.174 Sensitivity UNAFold: 0.492 NanoFolder: 0.207 Positive Predictive Value UNAFold: 0.506 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.498 RSpredict(seed): 0.363 Sensitivity UNAFold: 0.488 RSpredict(seed): 0.222 Positive Predictive Value UNAFold: 0.509 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.438 Mastr(20): 0.035 Sensitivity UNAFold: 0.435 Mastr(20): 0.002 Positive Predictive Value UNAFold: 0.442 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.531 Mastr(seed): 0.040 Sensitivity UNAFold: 0.519 Mastr(seed): 0.002 Positive Predictive Value UNAFold: 0.544 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.575 UNAFold: 0.483 Sensitivity Multilign(seed): 0.536 UNAFold: 0.457 Positive Predictive Value Multilign(seed): 0.625 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.666 UNAFold: 0.483 Sensitivity PPfold(seed): 0.536 UNAFold: 0.457 Positive Predictive Value PPfold(seed): 0.833 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.423 MCFold: 0.290 Sensitivity UNAFold: 0.394 MCFold: 0.320 Positive Predictive Value UNAFold: 0.463 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(seed)	10 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.650 TurboFold(seed): 0.633 Sensitivity PETfold_pre2.0(seed): 0.584 TurboFold(seed): 0.562 Positive Predictive Value PETfold_pre2.0(seed): 0.727 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71508538796e-06	10 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.633 ContextFold: 0.602 Sensitivity TurboFold(seed): 0.562 ContextFold: 0.554 Positive Predictive Value TurboFold(seed): 0.716 ContextFold: 0.658 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.23631009584e-09	10 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 TurboFold(seed): 0.633 Sensitivity CentroidAlifold(seed): 0.584 TurboFold(seed): 0.562 Positive Predictive Value CentroidAlifold(seed): 0.883 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.20029949774e-10	10 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.649 TurboFold(seed): 0.633 Sensitivity CentroidHomfold‑LAST: 0.562 TurboFold(seed): 0.562 Positive Predictive Value CentroidHomfold‑LAST: 0.753 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.45329040827e-07	0 TurboFold(seed) vs TurboFold(20) Matthews Correlation Coefficient TurboFold(seed): N/A TurboFold(20): N/A Sensitivity TurboFold(seed): N/A TurboFold(20): N/A Positive Predictive Value TurboFold(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(20): N/A Sensitivity TurboFold(seed): N/A PPfold(20): N/A Positive Predictive Value TurboFold(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.911 TurboFold(seed): 0.587 Sensitivity Cylofold: 0.914 TurboFold(seed): 0.513 Positive Predictive Value Cylofold: 0.908 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A CentroidAlifold(20): N/A Sensitivity TurboFold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value TurboFold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.646 TurboFold(seed): 0.633 Sensitivity IPknot: 0.592 TurboFold(seed): 0.562 Positive Predictive Value IPknot: 0.708 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.01818206431e-06	9 Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.870 TurboFold(seed): 0.600 Sensitivity Pknots: 0.887 TurboFold(seed): 0.518 Positive Predictive Value Pknots: 0.856 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 MXScarna(seed): 0.505 Sensitivity TurboFold(seed): 0.562 MXScarna(seed): 0.472 Positive Predictive Value TurboFold(seed): 0.716 MXScarna(seed): 0.545 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.85673856424e-11	0 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A RNAalifold(20): N/A Sensitivity TurboFold(seed): N/A RNAalifold(20): N/A Positive Predictive Value TurboFold(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.633 CentroidFold: 0.627 Sensitivity TurboFold(seed): 0.562 CentroidFold: 0.567 Positive Predictive Value TurboFold(seed): 0.716 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000331720066723	9 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.615 TurboFold(seed): 0.600 Sensitivity RNASampler(seed): 0.548 TurboFold(seed): 0.518 Positive Predictive Value RNASampler(seed): 0.697 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(20): N/A Sensitivity TurboFold(seed): N/A Multilign(20): N/A Positive Predictive Value TurboFold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.638 TurboFold(seed): 0.633 Sensitivity RNAalifold(seed): 0.515 TurboFold(seed): 0.562 Positive Predictive Value RNAalifold(seed): 0.795 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00654937862799	0 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): N/A TurboFold(seed): N/A Sensitivity RNASampler(20): N/A TurboFold(seed): N/A Positive Predictive Value RNASampler(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): N/A MXScarna(20): N/A Sensitivity TurboFold(seed): N/A MXScarna(20): N/A Positive Predictive Value TurboFold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.633 Contrafold: 0.590 Sensitivity TurboFold(seed): 0.562 Contrafold: 0.558 Positive Predictive Value TurboFold(seed): 0.716 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.9460272886e-09	0 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.633 Sfold: 0.512 Sensitivity TurboFold(seed): 0.562 Sfold: 0.489 Positive Predictive Value TurboFold(seed): 0.716 Sfold: 0.540 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	10 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.633 ProbKnot: 0.558 Sensitivity TurboFold(seed): 0.562 ProbKnot: 0.554 Positive Predictive Value TurboFold(seed): 0.716 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	10 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.633 MaxExpect: 0.563 Sensitivity TurboFold(seed): 0.562 MaxExpect: 0.549 Positive Predictive Value TurboFold(seed): 0.716 MaxExpect: 0.582 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.42028829171e-09	10 McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.807 TurboFold(seed): 0.633 Sensitivity McQFold: 0.803 TurboFold(seed): 0.562 Positive Predictive Value McQFold: 0.813 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.40200680498e-09	9 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Murlet(seed): 0.477 Sensitivity TurboFold(seed): 0.518 Murlet(seed): 0.333 Positive Predictive Value TurboFold(seed): 0.702 Murlet(seed): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.633 Fold: 0.510 Sensitivity TurboFold(seed): 0.562 Fold: 0.502 Positive Predictive Value TurboFold(seed): 0.716 Fold: 0.522 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.61358433984e-08	10 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.849 TurboFold(seed): 0.633 Sensitivity PknotsRG: 0.850 TurboFold(seed): 0.562 Positive Predictive Value PknotsRG: 0.850 TurboFold(seed): 0.716 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.00353292907e-09	10 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.633 UNAFold: 0.510 Sensitivity TurboFold(seed): 0.562 UNAFold: 0.494 Positive Predictive Value TurboFold(seed): 0.716 UNAFold: 0.532 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08		+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAsubopt: 0.470 Sensitivity TurboFold(seed): 0.562 RNAsubopt: 0.459 Positive Predictive Value TurboFold(seed): 0.716 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.38194587311e-08	? TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.628 Afold: 0.513 Sensitivity TurboFold(seed): 0.563 Afold: 0.493 Positive Predictive Value TurboFold(seed): 0.703 Afold: 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.633 RNASLOpt: 0.529 Sensitivity TurboFold(seed): 0.562 RNASLOpt: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNASLOpt: 0.586 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.07842257011e-08	+ TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAfold: 0.502 Sensitivity TurboFold(seed): 0.562 RNAfold: 0.494 Positive Predictive Value TurboFold(seed): 0.716 RNAfold: 0.516 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.41551907097e-09	? TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.600 HotKnots: 0.543 Sensitivity TurboFold(seed): 0.518 HotKnots: 0.560 Positive Predictive Value TurboFold(seed): 0.702 HotKnots: 0.534 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs TurboFold(seed) Matthews Correlation Coefficient RDfolder: 0.603 TurboFold(seed): 0.600 Sensitivity RDfolder: 0.512 TurboFold(seed): 0.518 Positive Predictive Value RDfolder: 0.717 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 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	+ TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAshapes: 0.496 Sensitivity TurboFold(seed): 0.562 RNAshapes: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.25253056981e-08	+ TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.633 CRWrnafold: 0.438 Sensitivity TurboFold(seed): 0.562 CRWrnafold: 0.425 Positive Predictive Value TurboFold(seed): 0.716 CRWrnafold: 0.456 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.02007144414e-09	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): N/A Carnac(20): N/A Sensitivity TurboFold(seed): N/A Carnac(20): N/A Positive Predictive Value TurboFold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.633 Vsfold5: 0.379 Sensitivity TurboFold(seed): 0.562 Vsfold5: 0.369 Positive Predictive Value TurboFold(seed): 0.716 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.52577670387e-09	+ TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.633 Vsfold4: 0.257 Sensitivity TurboFold(seed): 0.562 Vsfold4: 0.240 Positive Predictive Value TurboFold(seed): 0.716 Vsfold4: 0.283 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAwolf: 0.497 Sensitivity TurboFold(seed): 0.562 RNAwolf: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNAwolf: 0.519 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	? CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.589 TurboFold(seed): 0.569 Sensitivity CMfinder(seed): 0.455 TurboFold(seed): 0.508 Positive Predictive Value CMfinder(seed): 0.769 TurboFold(seed): 0.644 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 Carnac(seed): 0.485 Sensitivity TurboFold(seed): 0.562 Carnac(seed): 0.245 Positive Predictive Value TurboFold(seed): 0.716 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71210682542e-09	? RSpredict(20) vs TurboFold(seed) Matthews Correlation Coefficient RSpredict(20): N/A TurboFold(seed): N/A Sensitivity RSpredict(20): N/A TurboFold(seed): N/A Positive Predictive Value RSpredict(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.600 Alterna: 0.428 Sensitivity TurboFold(seed): 0.518 Alterna: 0.399 Positive Predictive Value TurboFold(seed): 0.702 Alterna: 0.469 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.709 NanoFolder: 0.585 Sensitivity TurboFold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value TurboFold(seed): 0.906 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 RSpredict(seed): 0.396 Sensitivity TurboFold(seed): 0.562 RSpredict(seed): 0.309 Positive Predictive Value TurboFold(seed): 0.716 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.12417824077e-10	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): N/A Mastr(20): N/A Sensitivity TurboFold(seed): N/A Mastr(20): N/A Positive Predictive Value TurboFold(seed): N/A Mastr(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 Mastr(seed): 0.420 Sensitivity TurboFold(seed): 0.562 Mastr(seed): 0.270 Positive Predictive Value TurboFold(seed): 0.716 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.644 Multilign(seed): 0.575 Sensitivity TurboFold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value TurboFold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 TurboFold(seed): 0.644 Sensitivity PPfold(seed): 0.536 TurboFold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 TurboFold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.600 MCFold: 0.343 Sensitivity TurboFold(seed): 0.518 MCFold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 MCFold: 0.302 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
RNAsubopt	523 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 RNAsubopt: 0.468 Sensitivity PETfold_pre2.0(seed): 0.592 RNAsubopt: 0.474 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RNAsubopt: 0.464 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.726 RNAsubopt: 0.473 Sensitivity ContextFold: 0.683 RNAsubopt: 0.480 Positive Predictive Value ContextFold: 0.773 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	290 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 RNAsubopt: 0.534 Sensitivity CentroidAlifold(seed): 0.524 RNAsubopt: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.920 RNAsubopt: 0.538 Number of pairs reference - predicted secondary structure: 290 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAsubopt: 0.473 Sensitivity CentroidHomfold‑LAST: 0.468 RNAsubopt: 0.480 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.741 RNAsubopt: 0.520 Sensitivity TurboFold(20): 0.685 RNAsubopt: 0.518 Positive Predictive Value TurboFold(20): 0.802 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAsubopt: 0.520 Sensitivity PETfold_pre2.0(20): 0.653 RNAsubopt: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.830 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.735 RNAsubopt: 0.520 Sensitivity PPfold(20): 0.635 RNAsubopt: 0.518 Positive Predictive Value PPfold(20): 0.851 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.701 RNAsubopt: 0.475 Sensitivity Cylofold: 0.673 RNAsubopt: 0.442 Positive Predictive Value Cylofold: 0.734 RNAsubopt: 0.518 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAsubopt: 0.520 Sensitivity CentroidAlifold(20): 0.562 RNAsubopt: 0.518 Positive Predictive Value CentroidAlifold(20): 0.917 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.603 RNAsubopt: 0.473 Sensitivity IPknot: 0.546 RNAsubopt: 0.480 Positive Predictive Value IPknot: 0.667 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.697 RNAsubopt: 0.470 Sensitivity Pknots: 0.668 RNAsubopt: 0.435 Positive Predictive Value Pknots: 0.733 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.598 RNAsubopt: 0.535 Sensitivity MXScarna(seed): 0.480 RNAsubopt: 0.532 Positive Predictive Value MXScarna(seed): 0.747 RNAsubopt: 0.539 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.661 RNAsubopt: 0.520 Sensitivity RNAalifold(20): 0.533 RNAsubopt: 0.518 Positive Predictive Value RNAalifold(20): 0.820 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.574 RNAsubopt: 0.473 Sensitivity CentroidFold: 0.518 RNAsubopt: 0.480 Positive Predictive Value CentroidFold: 0.636 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAsubopt: 0.463 Sensitivity RNASampler(seed): 0.572 RNAsubopt: 0.446 Positive Predictive Value RNASampler(seed): 0.755 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.34821445183e-08	196 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.651 RNAsubopt: 0.518 Sensitivity Multilign(20): 0.591 RNAsubopt: 0.516 Positive Predictive Value Multilign(20): 0.718 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	291 RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 RNAalifold(seed): 0.473 Sensitivity RNAsubopt: 0.530 RNAalifold(seed): 0.276 Positive Predictive Value RNAsubopt: 0.538 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 291 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.553 RNAsubopt: 0.369 Sensitivity RNASampler(20): 0.434 RNAsubopt: 0.377 Positive Predictive Value RNASampler(20): 0.705 RNAsubopt: 0.362 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.627 RNAsubopt: 0.520 Sensitivity MXScarna(20): 0.553 RNAsubopt: 0.518 Positive Predictive Value MXScarna(20): 0.713 RNAsubopt: 0.523 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.555 RNAsubopt: 0.473 Sensitivity Contrafold: 0.541 RNAsubopt: 0.480 Positive Predictive Value Contrafold: 0.571 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.550 RNAsubopt: 0.501 Sensitivity Murlet(20): 0.416 RNAsubopt: 0.500 Positive Predictive Value Murlet(20): 0.727 RNAsubopt: 0.503 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.516 RNAsubopt: 0.473 Sensitivity Sfold: 0.465 RNAsubopt: 0.480 Positive Predictive Value Sfold: 0.574 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.524 RNAsubopt: 0.473 Sensitivity ProbKnot: 0.519 RNAsubopt: 0.480 Positive Predictive Value ProbKnot: 0.532 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.525 RNAsubopt: 0.473 Sensitivity MaxExpect: 0.511 RNAsubopt: 0.480 Positive Predictive Value MaxExpect: 0.541 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.473 McQFold: 0.459 Sensitivity RNAsubopt: 0.480 McQFold: 0.449 Positive Predictive Value RNAsubopt: 0.468 McQFold: 0.472 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): 0.482 RNAsubopt: 0.463 Sensitivity Murlet(seed): 0.319 RNAsubopt: 0.446 Positive Predictive Value Murlet(seed): 0.734 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.38571919282e-05	627 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.499 RNAsubopt: 0.473 Sensitivity Fold: 0.500 RNAsubopt: 0.480 Positive Predictive Value Fold: 0.499 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.479 RNAsubopt: 0.473 Sensitivity PknotsRG: 0.480 RNAsubopt: 0.480 Positive Predictive Value PknotsRG: 0.480 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.478 RNAsubopt: 0.473 Sensitivity UNAFold: 0.474 RNAsubopt: 0.480 Positive Predictive Value UNAFold: 0.483 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAsubopt: 0.470 Sensitivity TurboFold(seed): 0.562 RNAsubopt: 0.459 Positive Predictive Value TurboFold(seed): 0.716 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.38194587311e-08		+ RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.514 Afold: 0.499 Sensitivity RNAsubopt: 0.516 Afold: 0.493 Positive Predictive Value RNAsubopt: 0.514 Afold: 0.508 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.466 RNASLOpt: 0.446 Sensitivity RNAsubopt: 0.473 RNASLOpt: 0.421 Positive Predictive Value RNAsubopt: 0.462 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.478 RNAsubopt: 0.473 Sensitivity RNAfold: 0.479 RNAsubopt: 0.480 Positive Predictive Value RNAfold: 0.479 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.453 RNAsubopt: 0.394 Sensitivity HotKnots: 0.445 RNAsubopt: 0.378 Positive Predictive Value HotKnots: 0.469 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: 0.508 RNAsubopt: 0.470 Sensitivity RDfolder: 0.432 RNAsubopt: 0.435 Positive Predictive Value RDfolder: 0.609 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.520 CMfinder(20): 0.482 Sensitivity RNAsubopt: 0.518 CMfinder(20): 0.310 Positive Predictive Value RNAsubopt: 0.523 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.470 RNAshapes: 0.408 Sensitivity RNAsubopt: 0.477 RNAshapes: 0.404 Positive Predictive Value RNAsubopt: 0.466 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.473 CRWrnafold: 0.422 Sensitivity RNAsubopt: 0.480 CRWrnafold: 0.424 Positive Predictive Value RNAsubopt: 0.468 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.520 Carnac(20): 0.365 Sensitivity RNAsubopt: 0.518 Carnac(20): 0.155 Positive Predictive Value RNAsubopt: 0.523 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.469 Vsfold5: 0.333 Sensitivity RNAsubopt: 0.475 Vsfold5: 0.317 Positive Predictive Value RNAsubopt: 0.464 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.469 Vsfold4: 0.337 Sensitivity RNAsubopt: 0.476 Vsfold4: 0.310 Positive Predictive Value RNAsubopt: 0.464 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.473 RNAwolf: 0.339 Sensitivity RNAsubopt: 0.480 RNAwolf: 0.354 Positive Predictive Value RNAsubopt: 0.468 RNAwolf: 0.327 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.490 CMfinder(seed): 0.363 Sensitivity RNAsubopt: 0.496 CMfinder(seed): 0.184 Positive Predictive Value RNAsubopt: 0.486 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.487 Carnac(seed): 0.146 Sensitivity RNAsubopt: 0.495 Carnac(seed): 0.022 Positive Predictive Value RNAsubopt: 0.481 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.520 RSpredict(20): 0.350 Sensitivity RNAsubopt: 0.518 RSpredict(20): 0.222 Positive Predictive Value RNAsubopt: 0.523 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.470 Alterna: 0.393 Sensitivity RNAsubopt: 0.435 Alterna: 0.365 Positive Predictive Value RNAsubopt: 0.520 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.504 NanoFolder: 0.176 Sensitivity RNAsubopt: 0.509 NanoFolder: 0.209 Positive Predictive Value RNAsubopt: 0.501 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 RSpredict(seed): 0.065 Sensitivity RNAsubopt: 0.531 RSpredict(seed): 0.017 Positive Predictive Value RNAsubopt: 0.539 RSpredict(seed): 0.254 Number of pairs reference - predicted secondary structure: 293 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.520 Mastr(20): 0.044 Sensitivity RNAsubopt: 0.518 Mastr(20): 0.003 Positive Predictive Value RNAsubopt: 0.523 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.535 Mastr(seed): 0.042 Sensitivity RNAsubopt: 0.533 Mastr(seed): 0.003 Positive Predictive Value RNAsubopt: 0.538 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.575 RNAsubopt: 0.478 Sensitivity Multilign(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.666 RNAsubopt: 0.478 Sensitivity PPfold(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.416 MCFold: 0.290 Sensitivity RNAsubopt: 0.393 MCFold: 0.320 Positive Predictive Value RNAsubopt: 0.451 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	375 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 Afold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.680 Afold: 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.800 Afold: 0.452 Number of pairs reference - predicted secondary structure: 375 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.692 Afold: 0.408 Sensitivity ContextFold: 0.648 Afold: 0.406 Positive Predictive Value ContextFold: 0.739 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	306 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 Afold: 0.483 Sensitivity CentroidAlifold(seed): 0.620 Afold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.907 Afold: 0.493 Number of pairs reference - predicted secondary structure: 306 Wilcoxon single-rank test P-value: 3.56938820447e-08	362 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.651 Afold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.486 Afold: 0.493 Positive Predictive Value CentroidHomfold‑LAST: 0.873 Afold: 0.508 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08	155 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.756 Afold: 0.548 Sensitivity TurboFold(20): 0.699 Afold: 0.533 Positive Predictive Value TurboFold(20): 0.819 Afold: 0.565 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.734 Afold: 0.453 Sensitivity PETfold_pre2.0(20): 0.687 Afold: 0.449 Positive Predictive Value PETfold_pre2.0(20): 0.785 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	153 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.744 Afold: 0.529 Sensitivity PPfold(20): 0.650 Afold: 0.514 Positive Predictive Value PPfold(20): 0.852 Afold: 0.544 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Cylofold vs Afold Matthews Correlation Coefficient Cylofold: 0.653 Afold: 0.349 Sensitivity Cylofold: 0.630 Afold: 0.334 Positive Predictive Value Cylofold: 0.682 Afold: 0.372 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Afold: 0.453 Sensitivity CentroidAlifold(20): 0.597 Afold: 0.449 Positive Predictive Value CentroidAlifold(20): 0.879 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	594 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.534 Afold: 0.409 Sensitivity IPknot: 0.462 Afold: 0.407 Positive Predictive Value IPknot: 0.618 Afold: 0.412 Number of pairs reference - predicted secondary structure: 594 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.653 Afold: 0.309 Sensitivity Pknots: 0.630 Afold: 0.296 Positive Predictive Value Pknots: 0.684 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	309 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.629 Afold: 0.484 Sensitivity MXScarna(seed): 0.535 Afold: 0.475 Positive Predictive Value MXScarna(seed): 0.741 Afold: 0.494 Number of pairs reference - predicted secondary structure: 309 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.671 Afold: 0.453 Sensitivity RNAalifold(20): 0.592 Afold: 0.449 Positive Predictive Value RNAalifold(20): 0.760 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	564 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.507 Afold: 0.413 Sensitivity CentroidFold: 0.439 Afold: 0.410 Positive Predictive Value CentroidFold: 0.586 Afold: 0.416 Number of pairs reference - predicted secondary structure: 564 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.642 Afold: 0.454 Sensitivity RNASampler(seed): 0.561 Afold: 0.427 Positive Predictive Value RNASampler(seed): 0.740 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.77512146924e-08	149 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.654 Afold: 0.545 Sensitivity Multilign(20): 0.592 Afold: 0.530 Positive Predictive Value Multilign(20): 0.724 Afold: 0.562 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	310 RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.637 Afold: 0.478 Sensitivity RNAalifold(seed): 0.496 Afold: 0.470 Positive Predictive Value RNAalifold(seed): 0.817 Afold: 0.486 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.541 Afold: 0.489 Sensitivity RNASampler(20): 0.411 Afold: 0.481 Positive Predictive Value RNASampler(20): 0.715 Afold: 0.499 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	228 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.612 Afold: 0.453 Sensitivity MXScarna(20): 0.551 Afold: 0.449 Positive Predictive Value MXScarna(20): 0.680 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.494 Afold: 0.408 Sensitivity Contrafold: 0.472 Afold: 0.406 Positive Predictive Value Contrafold: 0.517 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.555 Afold: 0.501 Sensitivity Murlet(20): 0.432 Afold: 0.491 Positive Predictive Value Murlet(20): 0.715 Afold: 0.512 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.454 Afold: 0.408 Sensitivity Sfold: 0.400 Afold: 0.406 Positive Predictive Value Sfold: 0.516 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.437 Afold: 0.408 Sensitivity ProbKnot: 0.430 Afold: 0.406 Positive Predictive Value ProbKnot: 0.445 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.443 Afold: 0.408 Sensitivity MaxExpect: 0.428 Afold: 0.406 Positive Predictive Value MaxExpect: 0.459 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	399 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.486 McQFold: 0.457 Sensitivity Afold: 0.481 McQFold: 0.443 Positive Predictive Value Afold: 0.492 McQFold: 0.473 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Murlet(seed) vs Afold Matthews Correlation Coefficient Murlet(seed): 0.588 Afold: 0.400 Sensitivity Murlet(seed): 0.501 Afold: 0.390 Positive Predictive Value Murlet(seed): 0.692 Afold: 0.412 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.70887622364e-08	595 Fold vs Afold Matthews Correlation Coefficient Fold: 0.413 Afold: 0.408 Sensitivity Fold: 0.415 Afold: 0.406 Positive Predictive Value Fold: 0.411 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	528 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.435 PknotsRG: 0.432 Sensitivity Afold: 0.429 PknotsRG: 0.428 Positive Predictive Value Afold: 0.441 PknotsRG: 0.437 Number of pairs reference - predicted secondary structure: 528 Wilcoxon single-rank test P-value: 1.47584956762e-07	595 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.416 Afold: 0.408 Sensitivity UNAFold: 0.412 Afold: 0.406 Positive Predictive Value UNAFold: 0.421 Afold: 0.411 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.628 Afold: 0.513 Sensitivity TurboFold(seed): 0.563 Afold: 0.493 Positive Predictive Value TurboFold(seed): 0.703 Afold: 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	362 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.514 Afold: 0.499 Sensitivity RNAsubopt: 0.516 Afold: 0.493 Positive Predictive Value RNAsubopt: 0.514 Afold: 0.508 Number of pairs reference - predicted secondary structure: 362 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.494 RNASLOpt: 0.464 Sensitivity Afold: 0.486 RNASLOpt: 0.430 Positive Predictive Value Afold: 0.503 RNASLOpt: 0.503 Number of pairs reference - predicted secondary structure: 309 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.408 RNAfold: 0.405 Sensitivity Afold: 0.406 RNAfold: 0.404 Positive Predictive Value Afold: 0.411 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.390 Afold: 0.316 Sensitivity HotKnots: 0.385 Afold: 0.305 Positive Predictive Value HotKnots: 0.405 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	- RDfolder vs Afold Matthews Correlation Coefficient RDfolder: 0.480 Afold: 0.309 Sensitivity RDfolder: 0.418 Afold: 0.296 Positive Predictive Value RDfolder: 0.561 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.548 CMfinder(20): 0.500 Sensitivity Afold: 0.533 CMfinder(20): 0.327 Positive Predictive Value Afold: 0.565 CMfinder(20): 0.764 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.498 RNAshapes: 0.460 Sensitivity Afold: 0.491 RNAshapes: 0.449 Positive Predictive Value Afold: 0.508 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 331 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.426 CRWrnafold: 0.404 Sensitivity Afold: 0.421 CRWrnafold: 0.403 Positive Predictive Value Afold: 0.432 CRWrnafold: 0.406 Number of pairs reference - predicted secondary structure: 503 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.496 Afold: 0.453 Sensitivity Carnac(20): 0.276 Afold: 0.449 Positive Predictive Value Carnac(20): 0.893 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.497 Vsfold5: 0.368 Sensitivity Afold: 0.489 Vsfold5: 0.344 Positive Predictive Value Afold: 0.506 Vsfold5: 0.396 Number of pairs reference - predicted secondary structure: 334 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.495 Vsfold4: 0.377 Sensitivity Afold: 0.488 Vsfold4: 0.344 Positive Predictive Value Afold: 0.504 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.446 RNAwolf: 0.301 Sensitivity Afold: 0.439 RNAwolf: 0.312 Positive Predictive Value Afold: 0.453 RNAwolf: 0.292 Number of pairs reference - predicted secondary structure: 457 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.522 CMfinder(seed): 0.355 Sensitivity Afold: 0.512 CMfinder(seed): 0.182 Positive Predictive Value Afold: 0.533 CMfinder(seed): 0.696 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.501 Carnac(seed): 0.259 Sensitivity Afold: 0.499 Carnac(seed): 0.071 Positive Predictive Value Afold: 0.503 Carnac(seed): 0.937 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.453 RSpredict(20): 0.417 Sensitivity Afold: 0.449 RSpredict(20): 0.338 Positive Predictive Value Afold: 0.458 RSpredict(20): 0.515 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Alterna vs Afold Matthews Correlation Coefficient Alterna: 0.340 Afold: 0.309 Sensitivity Alterna: 0.326 Afold: 0.296 Positive Predictive Value Alterna: 0.369 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.524 NanoFolder: 0.172 Sensitivity Afold: 0.514 NanoFolder: 0.199 Positive Predictive Value Afold: 0.535 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.485 RSpredict(seed): 0.382 Sensitivity Afold: 0.476 RSpredict(seed): 0.240 Positive Predictive Value Afold: 0.495 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 302 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.440 Mastr(20): 0.030 Sensitivity Afold: 0.437 Mastr(20): 0.001 Positive Predictive Value Afold: 0.442 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 180 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.525 Mastr(seed): 0.038 Sensitivity Afold: 0.514 Mastr(seed): 0.002 Positive Predictive Value Afold: 0.537 Mastr(seed): 0.639 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.571 Afold: 0.480 Sensitivity Multilign(seed): 0.533 Afold: 0.443 Positive Predictive Value Multilign(seed): 0.619 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.664 Afold: 0.480 Sensitivity PPfold(seed): 0.533 Afold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.280 MCFold: 0.263 Sensitivity Afold: 0.274 MCFold: 0.294 Positive Predictive Value Afold: 0.299 MCFold: 0.247 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.000706081118372
RNASLOpt	457 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 RNASLOpt: 0.449 Sensitivity PETfold_pre2.0(seed): 0.607 RNASLOpt: 0.424 Positive Predictive Value PETfold_pre2.0(seed): 0.794 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 457 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.729 RNASLOpt: 0.445 Sensitivity ContextFold: 0.684 RNASLOpt: 0.419 Positive Predictive Value ContextFold: 0.777 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNASLOpt: 0.477 Sensitivity CentroidAlifold(seed): 0.540 RNASLOpt: 0.439 Positive Predictive Value CentroidAlifold(seed): 0.932 RNASLOpt: 0.521 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	533 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.643 RNASLOpt: 0.446 Sensitivity CentroidHomfold‑LAST: 0.479 RNASLOpt: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.865 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.736 RNASLOpt: 0.456 Sensitivity TurboFold(20): 0.681 RNASLOpt: 0.421 Positive Predictive Value TurboFold(20): 0.797 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 RNASLOpt: 0.456 Sensitivity PETfold_pre2.0(20): 0.658 RNASLOpt: 0.421 Positive Predictive Value PETfold_pre2.0(20): 0.828 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.738 RNASLOpt: 0.457 Sensitivity PPfold(20): 0.640 RNASLOpt: 0.421 Positive Predictive Value PPfold(20): 0.851 RNASLOpt: 0.497 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.701 RNASLOpt: 0.523 Sensitivity Cylofold: 0.673 RNASLOpt: 0.470 Positive Predictive Value Cylofold: 0.734 RNASLOpt: 0.590 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNASLOpt: 0.456 Sensitivity CentroidAlifold(20): 0.564 RNASLOpt: 0.421 Positive Predictive Value CentroidAlifold(20): 0.915 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.599 RNASLOpt: 0.445 Sensitivity IPknot: 0.539 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.666 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.697 RNASLOpt: 0.549 Sensitivity Pknots: 0.668 RNASLOpt: 0.489 Positive Predictive Value Pknots: 0.733 RNASLOpt: 0.626 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	250 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.617 RNASLOpt: 0.478 Sensitivity MXScarna(seed): 0.500 RNASLOpt: 0.440 Positive Predictive Value MXScarna(seed): 0.763 RNASLOpt: 0.521 Number of pairs reference - predicted secondary structure: 250 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.663 RNASLOpt: 0.456 Sensitivity RNAalifold(20): 0.537 RNASLOpt: 0.421 Positive Predictive Value RNAalifold(20): 0.819 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.565 RNASLOpt: 0.445 Sensitivity CentroidFold: 0.508 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.631 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNASLOpt: 0.584 Sensitivity RNASampler(seed): 0.572 RNASLOpt: 0.526 Positive Predictive Value RNASampler(seed): 0.755 RNASLOpt: 0.655 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.10032755566e-08	182 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.655 RNASLOpt: 0.456 Sensitivity Multilign(20): 0.597 RNASLOpt: 0.421 Positive Predictive Value Multilign(20): 0.719 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	246 RNASLOpt vs RNAalifold(seed) Matthews Correlation Coefficient RNASLOpt: 0.477 RNAalifold(seed): 0.470 Sensitivity RNASLOpt: 0.439 RNAalifold(seed): 0.273 Positive Predictive Value RNASLOpt: 0.520 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 246 Wilcoxon single-rank test P-value: 2.28033735003e-07	50 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.553 RNASLOpt: 0.386 Sensitivity RNASampler(20): 0.434 RNASLOpt: 0.366 Positive Predictive Value RNASampler(20): 0.705 RNASLOpt: 0.408 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.620 RNASLOpt: 0.456 Sensitivity MXScarna(20): 0.547 RNASLOpt: 0.421 Positive Predictive Value MXScarna(20): 0.705 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.546 RNASLOpt: 0.445 Sensitivity Contrafold: 0.531 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.563 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	136 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.557 RNASLOpt: 0.438 Sensitivity Murlet(20): 0.426 RNASLOpt: 0.406 Positive Predictive Value Murlet(20): 0.730 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.506 RNASLOpt: 0.445 Sensitivity Sfold: 0.455 RNASLOpt: 0.419 Positive Predictive Value Sfold: 0.565 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.520 RNASLOpt: 0.445 Sensitivity ProbKnot: 0.514 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.528 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.521 RNASLOpt: 0.445 Sensitivity MaxExpect: 0.506 RNASLOpt: 0.419 Positive Predictive Value MaxExpect: 0.538 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.457 RNASLOpt: 0.445 Sensitivity McQFold: 0.446 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.470 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Murlet(seed): 0.482 Sensitivity RNASLOpt: 0.526 Murlet(seed): 0.319 Positive Predictive Value RNASLOpt: 0.655 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.08252958266e-08	534 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.493 RNASLOpt: 0.445 Sensitivity Fold: 0.494 RNASLOpt: 0.419 Positive Predictive Value Fold: 0.494 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.468 RNASLOpt: 0.445 Sensitivity PknotsRG: 0.469 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.470 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.468 RNASLOpt: 0.445 Sensitivity UNAFold: 0.464 RNASLOpt: 0.419 Positive Predictive Value UNAFold: 0.474 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.633 RNASLOpt: 0.529 Sensitivity TurboFold(seed): 0.562 RNASLOpt: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNASLOpt: 0.586 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.07842257011e-08	533 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.466 RNASLOpt: 0.446 Sensitivity RNAsubopt: 0.473 RNASLOpt: 0.421 Positive Predictive Value RNAsubopt: 0.462 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	309 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.494 RNASLOpt: 0.464 Sensitivity Afold: 0.486 RNASLOpt: 0.430 Positive Predictive Value Afold: 0.503 RNASLOpt: 0.503 Number of pairs reference - predicted secondary structure: 309 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.470 RNASLOpt: 0.445 Sensitivity RNAfold: 0.470 RNASLOpt: 0.419 Positive Predictive Value RNAfold: 0.472 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.458 HotKnots: 0.453 Sensitivity RNASLOpt: 0.419 HotKnots: 0.445 Positive Predictive Value RNASLOpt: 0.508 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0110724108869	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.549 RDfolder: 0.508 Sensitivity RNASLOpt: 0.489 RDfolder: 0.432 Positive Predictive Value RNASLOpt: 0.626 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.492 RNASLOpt: 0.456 Sensitivity CMfinder(20): 0.321 RNASLOpt: 0.421 Positive Predictive Value CMfinder(20): 0.757 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.446 RNAshapes: 0.403 Sensitivity RNASLOpt: 0.421 RNAshapes: 0.398 Positive Predictive Value RNASLOpt: 0.475 RNAshapes: 0.409 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.445 CRWrnafold: 0.418 Sensitivity RNASLOpt: 0.419 CRWrnafold: 0.419 Positive Predictive Value RNASLOpt: 0.474 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.456 Carnac(20): 0.358 Sensitivity RNASLOpt: 0.421 Carnac(20): 0.150 Positive Predictive Value RNASLOpt: 0.496 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold5: 0.337 Sensitivity RNASLOpt: 0.421 Vsfold5: 0.320 Positive Predictive Value RNASLOpt: 0.474 Vsfold5: 0.356 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold4: 0.340 Sensitivity RNASLOpt: 0.421 Vsfold4: 0.313 Positive Predictive Value RNASLOpt: 0.474 Vsfold4: 0.371 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.445 RNAwolf: 0.336 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.351 Positive Predictive Value RNASLOpt: 0.474 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 CMfinder(seed): 0.373 Sensitivity RNASLOpt: 0.443 CMfinder(seed): 0.200 Positive Predictive Value RNASLOpt: 0.510 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Carnac(seed): 0.178 Sensitivity RNASLOpt: 0.425 Carnac(seed): 0.033 Positive Predictive Value RNASLOpt: 0.503 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.456 RSpredict(20): 0.355 Sensitivity RNASLOpt: 0.421 RSpredict(20): 0.227 Positive Predictive Value RNASLOpt: 0.496 RSpredict(20): 0.557 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.549 Alterna: 0.393 Sensitivity RNASLOpt: 0.489 Alterna: 0.365 Positive Predictive Value RNASLOpt: 0.626 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.464 NanoFolder: 0.181 Sensitivity RNASLOpt: 0.432 NanoFolder: 0.212 Positive Predictive Value RNASLOpt: 0.501 NanoFolder: 0.157 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.478 RSpredict(seed): 0.061 Sensitivity RNASLOpt: 0.440 RSpredict(seed): 0.015 Positive Predictive Value RNASLOpt: 0.521 RSpredict(seed): 0.244 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.456 Mastr(20): 0.047 Sensitivity RNASLOpt: 0.421 Mastr(20): 0.003 Positive Predictive Value RNASLOpt: 0.496 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.476 Mastr(seed): 0.046 Sensitivity RNASLOpt: 0.438 Mastr(seed): 0.003 Positive Predictive Value RNASLOpt: 0.518 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.588 Multilign(seed): 0.575 Sensitivity RNASLOpt: 0.514 Multilign(seed): 0.536 Positive Predictive Value RNASLOpt: 0.679 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.666 RNASLOpt: 0.588 Sensitivity PPfold(seed): 0.536 RNASLOpt: 0.514 Positive Predictive Value PPfold(seed): 0.833 RNASLOpt: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.489 MCFold: 0.290 Sensitivity RNASLOpt: 0.442 MCFold: 0.320 Positive Predictive Value RNASLOpt: 0.549 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	610 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.717 RNAfold: 0.439 Sensitivity PETfold_pre2.0(seed): 0.651 RNAfold: 0.440 Positive Predictive Value PETfold_pre2.0(seed): 0.790 RNAfold: 0.439 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.676 RNAfold: 0.407 Sensitivity ContextFold: 0.634 RNAfold: 0.408 Positive Predictive Value ContextFold: 0.722 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.746 RNAfold: 0.477 Sensitivity CentroidAlifold(seed): 0.615 RNAfold: 0.471 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAfold: 0.478 Sensitivity CentroidHomfold‑LAST: 0.468 RNAfold: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAfold: 0.479 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.741 RNAfold: 0.528 Sensitivity TurboFold(20): 0.685 RNAfold: 0.519 Positive Predictive Value TurboFold(20): 0.802 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RNAfold: 0.444 Sensitivity PETfold_pre2.0(20): 0.681 RNAfold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.783 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.736 RNAfold: 0.515 Sensitivity PPfold(20): 0.641 RNAfold: 0.507 Positive Predictive Value PPfold(20): 0.846 RNAfold: 0.525 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.701 RNAfold: 0.481 Sensitivity Cylofold: 0.673 RNAfold: 0.445 Positive Predictive Value Cylofold: 0.734 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RNAfold: 0.444 Sensitivity CentroidAlifold(20): 0.595 RNAfold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.879 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	909 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.538 RNAfold: 0.408 Sensitivity IPknot: 0.470 RNAfold: 0.409 Positive Predictive Value IPknot: 0.616 RNAfold: 0.407 Number of pairs reference - predicted secondary structure: 909 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.697 RNAfold: 0.476 Sensitivity Pknots: 0.668 RNAfold: 0.439 Positive Predictive Value Pknots: 0.733 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.628 RNAfold: 0.478 Sensitivity MXScarna(seed): 0.533 RNAfold: 0.471 Positive Predictive Value MXScarna(seed): 0.741 RNAfold: 0.485 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAfold: 0.444 Sensitivity RNAalifold(20): 0.588 RNAfold: 0.443 Positive Predictive Value RNAalifold(20): 0.760 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	862 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.505 RNAfold: 0.407 Sensitivity CentroidFold: 0.441 RNAfold: 0.408 Positive Predictive Value CentroidFold: 0.579 RNAfold: 0.405 Number of pairs reference - predicted secondary structure: 862 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAfold: 0.476 Sensitivity RNASampler(seed): 0.572 RNAfold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	196 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.651 RNAfold: 0.528 Sensitivity Multilign(20): 0.591 RNAfold: 0.519 Positive Predictive Value Multilign(20): 0.718 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	363 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.629 RNAfold: 0.472 Sensitivity RNAalifold(seed): 0.485 RNAfold: 0.466 Positive Predictive Value RNAalifold(seed): 0.816 RNAfold: 0.479 Number of pairs reference - predicted secondary structure: 363 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.553 RNAfold: 0.398 Sensitivity RNASampler(20): 0.434 RNAfold: 0.404 Positive Predictive Value RNASampler(20): 0.705 RNAfold: 0.395 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.608 RNAfold: 0.444 Sensitivity MXScarna(20): 0.550 RNAfold: 0.443 Positive Predictive Value MXScarna(20): 0.674 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.496 RNAfold: 0.407 Sensitivity Contrafold: 0.477 RNAfold: 0.408 Positive Predictive Value Contrafold: 0.515 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.566 RNAfold: 0.484 Sensitivity Murlet(20): 0.445 RNAfold: 0.480 Positive Predictive Value Murlet(20): 0.722 RNAfold: 0.490 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.451 RNAfold: 0.407 Sensitivity Sfold: 0.400 RNAfold: 0.408 Positive Predictive Value Sfold: 0.509 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.442 RNAfold: 0.407 Sensitivity ProbKnot: 0.437 RNAfold: 0.408 Positive Predictive Value ProbKnot: 0.448 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.447 RNAfold: 0.407 Sensitivity MaxExpect: 0.435 RNAfold: 0.408 Positive Predictive Value MaxExpect: 0.461 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.471 McQFold: 0.450 Sensitivity RNAfold: 0.472 McQFold: 0.440 Positive Predictive Value RNAfold: 0.471 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): 0.584 RNAfold: 0.414 Sensitivity Murlet(seed): 0.492 RNAfold: 0.405 Positive Predictive Value Murlet(seed): 0.694 RNAfold: 0.424 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	910 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.417 RNAfold: 0.407 Sensitivity Fold: 0.421 RNAfold: 0.408 Positive Predictive Value Fold: 0.414 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.428 RNAfold: 0.425 Sensitivity PknotsRG: 0.427 RNAfold: 0.425 Positive Predictive Value PknotsRG: 0.429 RNAfold: 0.427 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	910 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.414 RNAfold: 0.407 Sensitivity UNAFold: 0.412 RNAfold: 0.408 Positive Predictive Value UNAFold: 0.417 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 910 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAfold: 0.502 Sensitivity TurboFold(seed): 0.562 RNAfold: 0.494 Positive Predictive Value TurboFold(seed): 0.716 RNAfold: 0.516 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.41551907097e-09	627 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.478 RNAsubopt: 0.473 Sensitivity RNAfold: 0.479 RNAsubopt: 0.480 Positive Predictive Value RNAfold: 0.479 RNAsubopt: 0.468 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	595 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.408 RNAfold: 0.405 Sensitivity Afold: 0.406 RNAfold: 0.404 Positive Predictive Value Afold: 0.411 RNAfold: 0.406 Number of pairs reference - predicted secondary structure: 595 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.470 RNASLOpt: 0.445 Sensitivity RNAfold: 0.470 RNASLOpt: 0.419 Positive Predictive Value RNAfold: 0.472 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08		- HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.453 RNAfold: 0.409 Sensitivity HotKnots: 0.445 RNAfold: 0.390 Positive Predictive Value HotKnots: 0.469 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: 0.508 RNAfold: 0.476 Sensitivity RDfolder: 0.432 RNAfold: 0.439 Positive Predictive Value RDfolder: 0.609 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.528 CMfinder(20): 0.482 Sensitivity RNAfold: 0.519 CMfinder(20): 0.310 Positive Predictive Value RNAfold: 0.539 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.475 RNAshapes: 0.408 Sensitivity RNAfold: 0.475 RNAshapes: 0.404 Positive Predictive Value RNAfold: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.424 CRWrnafold: 0.395 Sensitivity RNAfold: 0.424 CRWrnafold: 0.398 Positive Predictive Value RNAfold: 0.425 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.496 RNAfold: 0.444 Sensitivity Carnac(20): 0.277 RNAfold: 0.443 Positive Predictive Value Carnac(20): 0.888 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.473 Vsfold5: 0.333 Sensitivity RNAfold: 0.473 Vsfold5: 0.317 Positive Predictive Value RNAfold: 0.474 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.474 Vsfold4: 0.337 Sensitivity RNAfold: 0.474 Vsfold4: 0.310 Positive Predictive Value RNAfold: 0.475 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.441 RNAwolf: 0.302 Sensitivity RNAfold: 0.441 RNAwolf: 0.316 Positive Predictive Value RNAfold: 0.443 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.466 CMfinder(seed): 0.363 Sensitivity RNAfold: 0.466 CMfinder(seed): 0.184 Positive Predictive Value RNAfold: 0.468 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.501 Carnac(seed): 0.253 Sensitivity RNAfold: 0.503 Carnac(seed): 0.068 Positive Predictive Value RNAfold: 0.500 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.444 RSpredict(20): 0.425 Sensitivity RNAfold: 0.443 RSpredict(20): 0.345 Positive Predictive Value RNAfold: 0.446 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.476 Alterna: 0.393 Sensitivity RNAfold: 0.439 Alterna: 0.365 Positive Predictive Value RNAfold: 0.528 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.493 NanoFolder: 0.174 Sensitivity RNAfold: 0.491 NanoFolder: 0.207 Positive Predictive Value RNAfold: 0.497 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.480 RSpredict(seed): 0.363 Sensitivity RNAfold: 0.473 RSpredict(seed): 0.222 Positive Predictive Value RNAfold: 0.487 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.439 Mastr(20): 0.035 Sensitivity RNAfold: 0.439 Mastr(20): 0.002 Positive Predictive Value RNAfold: 0.439 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.525 Mastr(seed): 0.040 Sensitivity RNAfold: 0.516 Mastr(seed): 0.002 Positive Predictive Value RNAfold: 0.535 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.575 RNAfold: 0.472 Sensitivity Multilign(seed): 0.536 RNAfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.666 RNAfold: 0.472 Sensitivity PPfold(seed): 0.536 RNAfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.417 MCFold: 0.290 Sensitivity RNAfold: 0.391 MCFold: 0.320 Positive Predictive Value RNAfold: 0.455 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
HotKnots	19 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 HotKnots: 0.575 Sensitivity PETfold_pre2.0(seed): 0.649 HotKnots: 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.824 HotKnots: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.41358941668e-08	53 HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.453 ContextFold: 0.447 Sensitivity HotKnots: 0.445 ContextFold: 0.407 Positive Predictive Value HotKnots: 0.469 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.282238742299	17 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 HotKnots: 0.603 Sensitivity CentroidAlifold(seed): 0.634 HotKnots: 0.588 Positive Predictive Value CentroidAlifold(seed): 0.933 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	53 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 HotKnots: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 HotKnots: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.592 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.857 HotKnots: 0.717 Sensitivity TurboFold(20): 0.744 HotKnots: 0.639 Positive Predictive Value TurboFold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 HotKnots: 0.717 Sensitivity PETfold_pre2.0(20): 0.759 HotKnots: 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.962 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.840 HotKnots: 0.717 Sensitivity PPfold(20): 0.737 HotKnots: 0.639 Positive Predictive Value PPfold(20): 0.961 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	45 Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: 0.764 HotKnots: 0.524 Sensitivity Cylofold: 0.742 HotKnots: 0.501 Positive Predictive Value Cylofold: 0.791 HotKnots: 0.560 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 HotKnots: 0.717 Sensitivity CentroidAlifold(20): 0.752 HotKnots: 0.639 Positive Predictive Value CentroidAlifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	53 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.489 HotKnots: 0.453 Sensitivity IPknot: 0.435 HotKnots: 0.445 Positive Predictive Value IPknot: 0.556 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.697 HotKnots: 0.534 Sensitivity Pknots: 0.668 HotKnots: 0.510 Positive Predictive Value Pknots: 0.733 HotKnots: 0.569 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.603 MXScarna(seed): 0.539 Sensitivity HotKnots: 0.588 MXScarna(seed): 0.501 Positive Predictive Value HotKnots: 0.624 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	5 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.844 HotKnots: 0.717 Sensitivity RNAalifold(20): 0.722 HotKnots: 0.639 Positive Predictive Value RNAalifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	53 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.482 HotKnots: 0.453 Sensitivity CentroidFold: 0.430 HotKnots: 0.445 Positive Predictive Value CentroidFold: 0.548 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.655 HotKnots: 0.522 Sensitivity RNASampler(seed): 0.572 HotKnots: 0.526 Positive Predictive Value RNASampler(seed): 0.755 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.49381627234e-08	5 Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.862 HotKnots: 0.717 Sensitivity Multilign(20): 0.752 HotKnots: 0.639 Positive Predictive Value Multilign(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	17 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.657 HotKnots: 0.603 Sensitivity RNAalifold(seed): 0.522 HotKnots: 0.588 Positive Predictive Value RNAalifold(seed): 0.833 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	5 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.840 HotKnots: 0.717 Sensitivity RNASampler(20): 0.714 HotKnots: 0.639 Positive Predictive Value RNASampler(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.837 HotKnots: 0.717 Sensitivity MXScarna(20): 0.752 HotKnots: 0.639 Positive Predictive Value MXScarna(20): 0.935 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	53 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.458 HotKnots: 0.453 Sensitivity Contrafold: 0.435 HotKnots: 0.445 Positive Predictive Value Contrafold: 0.491 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0452037747897	5 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.741 HotKnots: 0.717 Sensitivity Murlet(20): 0.594 HotKnots: 0.639 Positive Predictive Value Murlet(20): 0.929 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	53 HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.453 Sfold: 0.425 Sensitivity HotKnots: 0.445 Sfold: 0.377 Positive Predictive Value HotKnots: 0.469 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.459 HotKnots: 0.453 Sensitivity ProbKnot: 0.440 HotKnots: 0.445 Positive Predictive Value ProbKnot: 0.487 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 6.29366556486e-06	53 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.453 MaxExpect: 0.440 Sensitivity HotKnots: 0.445 MaxExpect: 0.414 Positive Predictive Value HotKnots: 0.469 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	53 McQFold vs HotKnots Matthews Correlation Coefficient McQFold: 0.594 HotKnots: 0.453 Sensitivity McQFold: 0.583 HotKnots: 0.445 Positive Predictive Value McQFold: 0.611 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.522 Murlet(seed): 0.482 Sensitivity HotKnots: 0.526 Murlet(seed): 0.319 Positive Predictive Value HotKnots: 0.524 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	53 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.453 HotKnots: 0.453 Sensitivity Fold: 0.431 HotKnots: 0.445 Positive Predictive Value Fold: 0.485 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.236874878136	53 PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.531 HotKnots: 0.453 Sensitivity PknotsRG: 0.525 HotKnots: 0.445 Positive Predictive Value PknotsRG: 0.544 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.453 UNAFold: 0.412 Sensitivity HotKnots: 0.445 UNAFold: 0.390 Positive Predictive Value HotKnots: 0.469 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.600 HotKnots: 0.543 Sensitivity TurboFold(seed): 0.518 HotKnots: 0.560 Positive Predictive Value TurboFold(seed): 0.702 HotKnots: 0.534 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	53 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.453 RNAsubopt: 0.394 Sensitivity HotKnots: 0.445 RNAsubopt: 0.378 Positive Predictive Value HotKnots: 0.469 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.390 Afold: 0.316 Sensitivity HotKnots: 0.385 Afold: 0.305 Positive Predictive Value HotKnots: 0.405 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	53 RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.458 HotKnots: 0.453 Sensitivity RNASLOpt: 0.419 HotKnots: 0.445 Positive Predictive Value RNASLOpt: 0.508 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0110724108869	53 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.453 RNAfold: 0.409 Sensitivity HotKnots: 0.445 RNAfold: 0.390 Positive Predictive Value HotKnots: 0.469 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.534 RDfolder: 0.508 Sensitivity HotKnots: 0.510 RDfolder: 0.432 Positive Predictive Value HotKnots: 0.569 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.779 HotKnots: 0.717 Sensitivity CMfinder(20): 0.617 HotKnots: 0.639 Positive Predictive Value CMfinder(20): 0.988 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.453 RNAshapes: 0.416 Sensitivity HotKnots: 0.445 RNAshapes: 0.395 Positive Predictive Value HotKnots: 0.469 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.453 CRWrnafold: 0.374 Sensitivity HotKnots: 0.445 CRWrnafold: 0.351 Positive Predictive Value HotKnots: 0.469 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.821 HotKnots: 0.717 Sensitivity Carnac(20): 0.684 HotKnots: 0.639 Positive Predictive Value Carnac(20): 0.989 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Vsfold5 vs HotKnots Matthews Correlation Coefficient Vsfold5: 0.534 HotKnots: 0.453 Sensitivity Vsfold5: 0.505 HotKnots: 0.445 Positive Predictive Value Vsfold5: 0.572 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.453 Vsfold4: 0.423 Sensitivity HotKnots: 0.445 Vsfold4: 0.380 Positive Predictive Value HotKnots: 0.469 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.453 RNAwolf: 0.362 Sensitivity HotKnots: 0.445 RNAwolf: 0.353 Positive Predictive Value HotKnots: 0.469 RNAwolf: 0.380 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: 0.456 CMfinder(seed): 0.443 Sensitivity HotKnots: 0.458 CMfinder(seed): 0.333 Positive Predictive Value HotKnots: 0.462 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00972644458282	- Carnac(seed) vs HotKnots Matthews Correlation Coefficient Carnac(seed): 0.582 HotKnots: 0.522 Sensitivity Carnac(seed): 0.354 HotKnots: 0.526 Positive Predictive Value Carnac(seed): 0.962 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	? HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.717 RSpredict(20): 0.672 Sensitivity HotKnots: 0.639 RSpredict(20): 0.549 Positive Predictive Value HotKnots: 0.810 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.534 Alterna: 0.393 Sensitivity HotKnots: 0.510 Alterna: 0.365 Positive Predictive Value HotKnots: 0.569 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.431 NanoFolder: 0.304 Sensitivity HotKnots: 0.416 NanoFolder: 0.343 Positive Predictive Value HotKnots: 0.457 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.603 RSpredict(seed): 0.514 Sensitivity HotKnots: 0.588 RSpredict(seed): 0.427 Positive Predictive Value HotKnots: 0.624 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	? HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.717 Mastr(20): 0.561 Sensitivity HotKnots: 0.639 Mastr(20): 0.459 Positive Predictive Value HotKnots: 0.810 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.603 Mastr(seed): 0.341 Sensitivity HotKnots: 0.588 Mastr(seed): 0.176 Positive Predictive Value HotKnots: 0.624 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.24270395587e-08	? Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.575 HotKnots: 0.566 Sensitivity Multilign(seed): 0.536 HotKnots: 0.586 Positive Predictive Value Multilign(seed): 0.625 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs HotKnots Matthews Correlation Coefficient PPfold(seed): 0.666 HotKnots: 0.566 Sensitivity PPfold(seed): 0.536 HotKnots: 0.586 Positive Predictive Value PPfold(seed): 0.833 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.480 MCFold: 0.290 Sensitivity HotKnots: 0.464 MCFold: 0.320 Positive Predictive Value HotKnots: 0.506 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	18 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 RDfolder: 0.586 Sensitivity PETfold_pre2.0(seed): 0.661 RDfolder: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.823 RDfolder: 0.682 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	46 RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: 0.508 ContextFold: 0.500 Sensitivity RDfolder: 0.432 ContextFold: 0.441 Positive Predictive Value RDfolder: 0.609 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00456661807577	16 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RDfolder: 0.616 Sensitivity CentroidAlifold(seed): 0.642 RDfolder: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.936 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.55268413083e-08	46 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 RDfolder: 0.508 Sensitivity CentroidHomfold‑LAST: 0.471 RDfolder: 0.432 Positive Predictive Value CentroidHomfold‑LAST: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 8.1815824276e-08	5 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.857 RDfolder: 0.664 Sensitivity TurboFold(20): 0.744 RDfolder: 0.586 Positive Predictive Value TurboFold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RDfolder: 0.664 Sensitivity PETfold_pre2.0(20): 0.759 RDfolder: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.962 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.840 RDfolder: 0.664 Sensitivity PPfold(20): 0.737 RDfolder: 0.586 Positive Predictive Value PPfold(20): 0.961 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	45 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.764 RDfolder: 0.505 Sensitivity Cylofold: 0.742 RDfolder: 0.429 Positive Predictive Value Cylofold: 0.791 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RDfolder: 0.664 Sensitivity CentroidAlifold(20): 0.752 RDfolder: 0.586 Positive Predictive Value CentroidAlifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.558 RDfolder: 0.508 Sensitivity IPknot: 0.501 RDfolder: 0.432 Positive Predictive Value IPknot: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.508 Sensitivity Pknots: 0.668 RDfolder: 0.432 Positive Predictive Value Pknots: 0.733 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: 0.616 MXScarna(seed): 0.514 Sensitivity RDfolder: 0.531 MXScarna(seed): 0.481 Positive Predictive Value RDfolder: 0.721 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.91763127434e-08	5 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.844 RDfolder: 0.664 Sensitivity RNAalifold(20): 0.722 RDfolder: 0.586 Positive Predictive Value RNAalifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.544 RDfolder: 0.508 Sensitivity CentroidFold: 0.485 RDfolder: 0.432 Positive Predictive Value CentroidFold: 0.621 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.85233844192e-08	12 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.641 RDfolder: 0.561 Sensitivity RNASampler(seed): 0.562 RDfolder: 0.481 Positive Predictive Value RNASampler(seed): 0.736 RDfolder: 0.663 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.84361416392e-08	5 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.862 RDfolder: 0.664 Sensitivity Multilign(20): 0.752 RDfolder: 0.586 Positive Predictive Value Multilign(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	16 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.651 RDfolder: 0.616 Sensitivity RNAalifold(seed): 0.519 RDfolder: 0.531 Positive Predictive Value RNAalifold(seed): 0.823 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.83464629825e-08	5 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.840 RDfolder: 0.664 Sensitivity RNASampler(20): 0.714 RDfolder: 0.586 Positive Predictive Value RNASampler(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.837 RDfolder: 0.664 Sensitivity MXScarna(20): 0.752 RDfolder: 0.586 Positive Predictive Value MXScarna(20): 0.935 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.515 RDfolder: 0.508 Sensitivity Contrafold: 0.477 RDfolder: 0.432 Positive Predictive Value Contrafold: 0.567 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0481694229406	5 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.741 RDfolder: 0.664 Sensitivity Murlet(20): 0.594 RDfolder: 0.586 Positive Predictive Value Murlet(20): 0.929 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: 0.508 Sfold: 0.482 Sensitivity RDfolder: 0.432 Sfold: 0.435 Positive Predictive Value RDfolder: 0.609 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.09925167801e-06	46 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.527 RDfolder: 0.508 Sensitivity ProbKnot: 0.496 RDfolder: 0.432 Positive Predictive Value ProbKnot: 0.570 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.53079410487e-06	46 RDfolder vs MaxExpect Matthews Correlation Coefficient RDfolder: 0.508 MaxExpect: 0.503 Sensitivity RDfolder: 0.432 MaxExpect: 0.463 Positive Predictive Value RDfolder: 0.609 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0738256256282	46 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.508 Sensitivity McQFold: 0.679 RDfolder: 0.432 Positive Predictive Value McQFold: 0.738 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.561 Murlet(seed): 0.432 Sensitivity RDfolder: 0.481 Murlet(seed): 0.283 Positive Predictive Value RDfolder: 0.663 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.43573297697e-08	46 RDfolder vs Fold Matthews Correlation Coefficient RDfolder: 0.508 Fold: 0.504 Sensitivity RDfolder: 0.432 Fold: 0.466 Positive Predictive Value RDfolder: 0.609 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0372146796483	46 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.627 RDfolder: 0.508 Sensitivity PknotsRG: 0.601 RDfolder: 0.432 Positive Predictive Value PknotsRG: 0.662 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs UNAFold Matthews Correlation Coefficient RDfolder: 0.508 UNAFold: 0.468 Sensitivity RDfolder: 0.432 UNAFold: 0.431 Positive Predictive Value RDfolder: 0.609 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	9 RDfolder vs TurboFold(seed) Matthews Correlation Coefficient RDfolder: 0.603 TurboFold(seed): 0.600 Sensitivity RDfolder: 0.512 TurboFold(seed): 0.518 Positive Predictive Value RDfolder: 0.717 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	46 RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: 0.508 RNAsubopt: 0.470 Sensitivity RDfolder: 0.432 RNAsubopt: 0.435 Positive Predictive Value RDfolder: 0.609 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 5.62644058675e-08	29 RDfolder vs Afold Matthews Correlation Coefficient RDfolder: 0.480 Afold: 0.309 Sensitivity RDfolder: 0.418 Afold: 0.296 Positive Predictive Value RDfolder: 0.561 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	46 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.549 RDfolder: 0.508 Sensitivity RNASLOpt: 0.489 RDfolder: 0.432 Positive Predictive Value RNASLOpt: 0.626 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: 0.508 RNAfold: 0.476 Sensitivity RDfolder: 0.432 RNAfold: 0.439 Positive Predictive Value RDfolder: 0.609 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.534 RDfolder: 0.508 Sensitivity HotKnots: 0.510 RDfolder: 0.432 Positive Predictive Value HotKnots: 0.569 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08		? CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.779 RDfolder: 0.664 Sensitivity CMfinder(20): 0.617 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.988 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: 0.508 RNAshapes: 0.463 Sensitivity RDfolder: 0.432 RNAshapes: 0.426 Positive Predictive Value RDfolder: 0.609 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: 0.508 CRWrnafold: 0.458 Sensitivity RDfolder: 0.432 CRWrnafold: 0.415 Positive Predictive Value RDfolder: 0.609 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.85233844192e-08	? Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.821 RDfolder: 0.664 Sensitivity Carnac(20): 0.684 RDfolder: 0.586 Positive Predictive Value Carnac(20): 0.989 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.597 RDfolder: 0.508 Sensitivity Vsfold5: 0.550 RDfolder: 0.432 Positive Predictive Value Vsfold5: 0.657 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: 0.508 Vsfold4: 0.480 Sensitivity RDfolder: 0.432 Vsfold4: 0.423 Positive Predictive Value RDfolder: 0.609 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 2.63254822069e-07	+ RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: 0.508 RNAwolf: 0.401 Sensitivity RDfolder: 0.432 RNAwolf: 0.381 Positive Predictive Value RDfolder: 0.609 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: 0.538 CMfinder(seed): 0.459 Sensitivity RDfolder: 0.472 CMfinder(seed): 0.365 Positive Predictive Value RDfolder: 0.620 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.561 Carnac(seed): 0.531 Sensitivity RDfolder: 0.481 Carnac(seed): 0.292 Positive Predictive Value RDfolder: 0.663 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.85159322687e-07	? RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.672 RDfolder: 0.664 Sensitivity RSpredict(20): 0.549 RDfolder: 0.586 Positive Predictive Value RSpredict(20): 0.830 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: 0.508 Alterna: 0.393 Sensitivity RDfolder: 0.432 Alterna: 0.365 Positive Predictive Value RDfolder: 0.609 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.466 NanoFolder: 0.304 Sensitivity RDfolder: 0.398 NanoFolder: 0.343 Positive Predictive Value RDfolder: 0.555 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.616 RSpredict(seed): 0.518 Sensitivity RDfolder: 0.531 RSpredict(seed): 0.437 Positive Predictive Value RDfolder: 0.721 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.66715895098e-08	? RDfolder vs Mastr(20) Matthews Correlation Coefficient RDfolder: 0.664 Mastr(20): 0.561 Sensitivity RDfolder: 0.586 Mastr(20): 0.459 Positive Predictive Value RDfolder: 0.757 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.616 Mastr(seed): 0.365 Sensitivity RDfolder: 0.531 Mastr(seed): 0.202 Positive Predictive Value RDfolder: 0.721 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	? RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: 0.593 Multilign(seed): 0.575 Sensitivity RDfolder: 0.486 Multilign(seed): 0.536 Positive Predictive Value RDfolder: 0.731 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RDfolder Matthews Correlation Coefficient PPfold(seed): 0.666 RDfolder: 0.593 Sensitivity PPfold(seed): 0.536 RDfolder: 0.486 Positive Predictive Value PPfold(seed): 0.833 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.505 MCFold: 0.296 Sensitivity RDfolder: 0.428 MCFold: 0.325 Positive Predictive Value RDfolder: 0.605 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	209 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(seed): 0.674 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.840 CMfinder(20): 0.482 Sensitivity ContextFold: 0.791 CMfinder(20): 0.310 Positive Predictive Value ContextFold: 0.892 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	166 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.723 CMfinder(20): 0.504 Sensitivity CentroidAlifold(seed): 0.550 CMfinder(20): 0.331 Positive Predictive Value CentroidAlifold(seed): 0.952 CMfinder(20): 0.771 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 CMfinder(20): 0.482 Sensitivity CentroidHomfold‑LAST: 0.552 CMfinder(20): 0.310 Positive Predictive Value CentroidHomfold‑LAST: 0.896 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.741 CMfinder(20): 0.482 Sensitivity TurboFold(20): 0.685 CMfinder(20): 0.310 Positive Predictive Value TurboFold(20): 0.802 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(20): 0.653 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(20): 0.830 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.735 CMfinder(20): 0.482 Sensitivity PPfold(20): 0.635 CMfinder(20): 0.311 Positive Predictive Value PPfold(20): 0.851 CMfinder(20): 0.750 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.779 Cylofold: 0.756 Sensitivity CMfinder(20): 0.617 Cylofold: 0.677 Positive Predictive Value CMfinder(20): 0.988 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	209 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.718 CMfinder(20): 0.482 Sensitivity CentroidAlifold(20): 0.562 CMfinder(20): 0.310 Positive Predictive Value CentroidAlifold(20): 0.917 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.649 CMfinder(20): 0.482 Sensitivity IPknot: 0.575 CMfinder(20): 0.310 Positive Predictive Value IPknot: 0.734 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.779 Pknots: 0.723 Sensitivity CMfinder(20): 0.617 Pknots: 0.632 Positive Predictive Value CMfinder(20): 0.988 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	168 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.656 CMfinder(20): 0.505 Sensitivity MXScarna(seed): 0.543 CMfinder(20): 0.331 Positive Predictive Value MXScarna(seed): 0.795 CMfinder(20): 0.770 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.661 CMfinder(20): 0.482 Sensitivity RNAalifold(20): 0.533 CMfinder(20): 0.310 Positive Predictive Value RNAalifold(20): 0.820 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.617 CMfinder(20): 0.482 Sensitivity CentroidFold: 0.548 CMfinder(20): 0.310 Positive Predictive Value CentroidFold: 0.696 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	196 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.651 CMfinder(20): 0.484 Sensitivity Multilign(20): 0.591 CMfinder(20): 0.312 Positive Predictive Value Multilign(20): 0.718 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	166 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.504 RNAalifold(seed): 0.448 Sensitivity CMfinder(20): 0.331 RNAalifold(seed): 0.252 Positive Predictive Value CMfinder(20): 0.771 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 166 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.553 CMfinder(20): 0.386 Sensitivity RNASampler(20): 0.434 CMfinder(20): 0.232 Positive Predictive Value RNASampler(20): 0.705 CMfinder(20): 0.644 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.627 CMfinder(20): 0.482 Sensitivity MXScarna(20): 0.553 CMfinder(20): 0.310 Positive Predictive Value MXScarna(20): 0.713 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.602 CMfinder(20): 0.482 Sensitivity Contrafold: 0.577 CMfinder(20): 0.310 Positive Predictive Value Contrafold: 0.630 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.550 CMfinder(20): 0.466 Sensitivity Murlet(20): 0.416 CMfinder(20): 0.296 Positive Predictive Value Murlet(20): 0.727 CMfinder(20): 0.733 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.569 CMfinder(20): 0.482 Sensitivity Sfold: 0.503 CMfinder(20): 0.310 Positive Predictive Value Sfold: 0.644 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.587 CMfinder(20): 0.482 Sensitivity ProbKnot: 0.565 CMfinder(20): 0.310 Positive Predictive Value ProbKnot: 0.611 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.588 CMfinder(20): 0.482 Sensitivity MaxExpect: 0.562 CMfinder(20): 0.310 Positive Predictive Value MaxExpect: 0.617 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.482 McQFold: 0.454 Sensitivity CMfinder(20): 0.310 McQFold: 0.434 Positive Predictive Value CMfinder(20): 0.749 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	209 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.551 CMfinder(20): 0.482 Sensitivity Fold: 0.542 CMfinder(20): 0.310 Positive Predictive Value Fold: 0.562 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.513 CMfinder(20): 0.482 Sensitivity PknotsRG: 0.504 CMfinder(20): 0.310 Positive Predictive Value PknotsRG: 0.524 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.532 CMfinder(20): 0.482 Sensitivity UNAFold: 0.520 CMfinder(20): 0.310 Positive Predictive Value UNAFold: 0.546 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	209 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.520 CMfinder(20): 0.482 Sensitivity RNAsubopt: 0.518 CMfinder(20): 0.310 Positive Predictive Value RNAsubopt: 0.523 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	155 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.548 CMfinder(20): 0.500 Sensitivity Afold: 0.533 CMfinder(20): 0.327 Positive Predictive Value Afold: 0.565 CMfinder(20): 0.764 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.492 RNASLOpt: 0.456 Sensitivity CMfinder(20): 0.321 RNASLOpt: 0.421 Positive Predictive Value CMfinder(20): 0.757 RNASLOpt: 0.496 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.528 CMfinder(20): 0.482 Sensitivity RNAfold: 0.519 CMfinder(20): 0.310 Positive Predictive Value RNAfold: 0.539 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.779 HotKnots: 0.717 Sensitivity CMfinder(20): 0.617 HotKnots: 0.639 Positive Predictive Value CMfinder(20): 0.988 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.779 RDfolder: 0.664 Sensitivity CMfinder(20): 0.617 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.988 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.491 RNAshapes: 0.457 Sensitivity CMfinder(20): 0.319 RNAshapes: 0.442 Positive Predictive Value CMfinder(20): 0.757 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.482 CRWrnafold: 0.456 Sensitivity CMfinder(20): 0.310 CRWrnafold: 0.447 Positive Predictive Value CMfinder(20): 0.749 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.482 Carnac(20): 0.365 Sensitivity CMfinder(20): 0.310 Carnac(20): 0.155 Positive Predictive Value CMfinder(20): 0.749 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.490 Vsfold5: 0.371 Sensitivity CMfinder(20): 0.318 Vsfold5: 0.344 Positive Predictive Value CMfinder(20): 0.756 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.488 Vsfold4: 0.392 Sensitivity CMfinder(20): 0.316 Vsfold4: 0.355 Positive Predictive Value CMfinder(20): 0.754 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.482 RNAwolf: 0.368 Sensitivity CMfinder(20): 0.310 RNAwolf: 0.378 Positive Predictive Value CMfinder(20): 0.749 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.140 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.085 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.232 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.482 RSpredict(20): 0.350 Sensitivity CMfinder(20): 0.310 RSpredict(20): 0.222 Positive Predictive Value CMfinder(20): 0.749 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.779 Alterna: 0.656 Sensitivity CMfinder(20): 0.617 Alterna: 0.602 Positive Predictive Value CMfinder(20): 0.988 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.487 NanoFolder: 0.152 Sensitivity CMfinder(20): 0.310 NanoFolder: 0.174 Positive Predictive Value CMfinder(20): 0.766 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.506 RSpredict(seed): 0.063 Sensitivity CMfinder(20): 0.333 RSpredict(seed): 0.016 Positive Predictive Value CMfinder(20): 0.771 RSpredict(seed): 0.246 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.482 Mastr(20): 0.044 Sensitivity CMfinder(20): 0.310 Mastr(20): 0.003 Positive Predictive Value CMfinder(20): 0.749 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.505 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.334 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.766 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-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	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.779 MCFold: 0.291 Sensitivity CMfinder(20): 0.617 MCFold: 0.323 Positive Predictive Value CMfinder(20): 0.988 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
RNAshapes	495 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.684 RNAshapes: 0.399 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.394 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAshapes: 0.405 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.730 RNAshapes: 0.408 Sensitivity ContextFold: 0.685 RNAshapes: 0.404 Positive Predictive Value ContextFold: 0.778 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	270 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 RNAshapes: 0.486 Sensitivity CentroidAlifold(seed): 0.528 RNAshapes: 0.470 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAshapes: 0.506 Number of pairs reference - predicted secondary structure: 270 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAshapes: 0.408 Sensitivity CentroidHomfold‑LAST: 0.474 RNAshapes: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.868 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.739 RNAshapes: 0.457 Sensitivity TurboFold(20): 0.683 RNAshapes: 0.442 Positive Predictive Value TurboFold(20): 0.800 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.738 RNAshapes: 0.457 Sensitivity PETfold_pre2.0(20): 0.655 RNAshapes: 0.442 Positive Predictive Value PETfold_pre2.0(20): 0.831 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	193 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.738 RNAshapes: 0.456 Sensitivity PPfold(20): 0.639 RNAshapes: 0.441 Positive Predictive Value PPfold(20): 0.854 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 193 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.701 RNAshapes: 0.471 Sensitivity Cylofold: 0.673 RNAshapes: 0.437 Positive Predictive Value Cylofold: 0.734 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAshapes: 0.457 Sensitivity CentroidAlifold(20): 0.562 RNAshapes: 0.442 Positive Predictive Value CentroidAlifold(20): 0.917 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.602 RNAshapes: 0.408 Sensitivity IPknot: 0.543 RNAshapes: 0.404 Positive Predictive Value IPknot: 0.668 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.697 RNAshapes: 0.463 Sensitivity Pknots: 0.668 RNAshapes: 0.426 Positive Predictive Value Pknots: 0.733 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.603 RNAshapes: 0.486 Sensitivity MXScarna(seed): 0.485 RNAshapes: 0.470 Positive Predictive Value MXScarna(seed): 0.751 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.663 RNAshapes: 0.457 Sensitivity RNAalifold(20): 0.535 RNAshapes: 0.442 Positive Predictive Value RNAalifold(20): 0.823 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.569 RNAshapes: 0.408 Sensitivity CentroidFold: 0.513 RNAshapes: 0.404 Positive Predictive Value CentroidFold: 0.633 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAshapes: 0.447 Sensitivity RNASampler(seed): 0.572 RNAshapes: 0.432 Positive Predictive Value RNASampler(seed): 0.755 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	187 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.651 RNAshapes: 0.454 Sensitivity Multilign(20): 0.592 RNAshapes: 0.440 Positive Predictive Value Multilign(20): 0.718 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	271 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.486 RNAalifold(seed): 0.467 Sensitivity RNAshapes: 0.469 RNAalifold(seed): 0.270 Positive Predictive Value RNAshapes: 0.505 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.553 RNAshapes: 0.315 Sensitivity RNASampler(20): 0.433 RNAshapes: 0.313 Positive Predictive Value RNASampler(20): 0.707 RNAshapes: 0.318 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.623 RNAshapes: 0.457 Sensitivity MXScarna(20): 0.548 RNAshapes: 0.442 Positive Predictive Value MXScarna(20): 0.709 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.550 RNAshapes: 0.408 Sensitivity Contrafold: 0.535 RNAshapes: 0.404 Positive Predictive Value Contrafold: 0.567 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	144 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.555 RNAshapes: 0.433 Sensitivity Murlet(20): 0.421 RNAshapes: 0.420 Positive Predictive Value Murlet(20): 0.734 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.511 RNAshapes: 0.408 Sensitivity Sfold: 0.460 RNAshapes: 0.404 Positive Predictive Value Sfold: 0.570 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.524 RNAshapes: 0.408 Sensitivity ProbKnot: 0.517 RNAshapes: 0.404 Positive Predictive Value ProbKnot: 0.532 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.524 RNAshapes: 0.408 Sensitivity MaxExpect: 0.509 RNAshapes: 0.404 Positive Predictive Value MaxExpect: 0.541 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.461 RNAshapes: 0.408 Sensitivity McQFold: 0.450 RNAshapes: 0.404 Positive Predictive Value McQFold: 0.475 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.482 RNAshapes: 0.447 Sensitivity Murlet(seed): 0.319 RNAshapes: 0.432 Positive Predictive Value Murlet(seed): 0.734 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.74910108057e-08	579 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.497 RNAshapes: 0.408 Sensitivity Fold: 0.498 RNAshapes: 0.404 Positive Predictive Value Fold: 0.498 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.476 RNAshapes: 0.408 Sensitivity PknotsRG: 0.476 RNAshapes: 0.404 Positive Predictive Value PknotsRG: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.474 RNAshapes: 0.408 Sensitivity UNAFold: 0.470 RNAshapes: 0.404 Positive Predictive Value UNAFold: 0.480 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAshapes: 0.496 Sensitivity TurboFold(seed): 0.562 RNAshapes: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.25253056981e-08	579 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.470 RNAshapes: 0.408 Sensitivity RNAsubopt: 0.477 RNAshapes: 0.404 Positive Predictive Value RNAsubopt: 0.466 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	331 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.498 RNAshapes: 0.460 Sensitivity Afold: 0.491 RNAshapes: 0.449 Positive Predictive Value Afold: 0.508 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 331 Wilcoxon single-rank test P-value: 3.56938820447e-08	527 RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.446 RNAshapes: 0.403 Sensitivity RNASLOpt: 0.421 RNAshapes: 0.398 Positive Predictive Value RNASLOpt: 0.475 RNAshapes: 0.409 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.475 RNAshapes: 0.408 Sensitivity RNAfold: 0.475 RNAshapes: 0.404 Positive Predictive Value RNAfold: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.453 RNAshapes: 0.416 Sensitivity HotKnots: 0.445 RNAshapes: 0.395 Positive Predictive Value HotKnots: 0.469 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: 0.508 RNAshapes: 0.463 Sensitivity RDfolder: 0.432 RNAshapes: 0.426 Positive Predictive Value RDfolder: 0.609 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.491 RNAshapes: 0.457 Sensitivity CMfinder(20): 0.319 RNAshapes: 0.442 Positive Predictive Value CMfinder(20): 0.757 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.420 RNAshapes: 0.408 Sensitivity CRWrnafold: 0.421 RNAshapes: 0.404 Positive Predictive Value CRWrnafold: 0.421 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.457 Carnac(20): 0.364 Sensitivity RNAshapes: 0.442 Carnac(20): 0.154 Positive Predictive Value RNAshapes: 0.474 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold5: 0.335 Sensitivity RNAshapes: 0.402 Vsfold5: 0.318 Positive Predictive Value RNAshapes: 0.412 Vsfold5: 0.355 Number of pairs reference - predicted secondary structure: 575 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold4: 0.340 Sensitivity RNAshapes: 0.402 Vsfold4: 0.313 Positive Predictive Value RNAshapes: 0.412 Vsfold4: 0.371 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.408 RNAwolf: 0.341 Sensitivity RNAshapes: 0.404 RNAwolf: 0.355 Positive Predictive Value RNAshapes: 0.414 RNAwolf: 0.329 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.540 CMfinder(seed): 0.359 Sensitivity RNAshapes: 0.531 CMfinder(seed): 0.186 Positive Predictive Value RNAshapes: 0.550 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.467 Carnac(seed): 0.169 Sensitivity RNAshapes: 0.458 Carnac(seed): 0.030 Positive Predictive Value RNAshapes: 0.478 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.457 RSpredict(20): 0.355 Sensitivity RNAshapes: 0.442 RSpredict(20): 0.226 Positive Predictive Value RNAshapes: 0.474 RSpredict(20): 0.558 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.463 Alterna: 0.393 Sensitivity RNAshapes: 0.426 Alterna: 0.365 Positive Predictive Value RNAshapes: 0.515 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.434 NanoFolder: 0.177 Sensitivity RNAshapes: 0.426 NanoFolder: 0.209 Positive Predictive Value RNAshapes: 0.444 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.486 RSpredict(seed): 0.060 Sensitivity RNAshapes: 0.469 RSpredict(seed): 0.015 Positive Predictive Value RNAshapes: 0.505 RSpredict(seed): 0.238 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.457 Mastr(20): 0.046 Sensitivity RNAshapes: 0.442 Mastr(20): 0.003 Positive Predictive Value RNAshapes: 0.474 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.482 Mastr(seed): 0.044 Sensitivity RNAshapes: 0.467 Mastr(seed): 0.003 Positive Predictive Value RNAshapes: 0.500 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.575 RNAshapes: 0.481 Sensitivity Multilign(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.666 RNAshapes: 0.481 Sensitivity PPfold(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.438 MCFold: 0.290 Sensitivity RNAshapes: 0.408 MCFold: 0.320 Positive Predictive Value RNAshapes: 0.481 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	556 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CRWrnafold: 0.437 Sensitivity PETfold_pre2.0(seed): 0.636 CRWrnafold: 0.437 Positive Predictive Value PETfold_pre2.0(seed): 0.804 CRWrnafold: 0.439 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.725 CRWrnafold: 0.395 Sensitivity ContextFold: 0.679 CRWrnafold: 0.398 Positive Predictive Value ContextFold: 0.773 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	323 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.743 CRWrnafold: 0.476 Sensitivity CentroidAlifold(seed): 0.604 CRWrnafold: 0.468 Positive Predictive Value CentroidAlifold(seed): 0.914 CRWrnafold: 0.486 Number of pairs reference - predicted secondary structure: 323 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 CRWrnafold: 0.422 Sensitivity CentroidHomfold‑LAST: 0.468 CRWrnafold: 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.870 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.741 CRWrnafold: 0.456 Sensitivity TurboFold(20): 0.685 CRWrnafold: 0.447 Positive Predictive Value TurboFold(20): 0.802 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.771 CRWrnafold: 0.484 Sensitivity PETfold_pre2.0(20): 0.710 CRWrnafold: 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.837 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.740 CRWrnafold: 0.464 Sensitivity PPfold(20): 0.643 CRWrnafold: 0.455 Positive Predictive Value PPfold(20): 0.852 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.701 CRWrnafold: 0.469 Sensitivity Cylofold: 0.673 CRWrnafold: 0.430 Positive Predictive Value Cylofold: 0.734 CRWrnafold: 0.519 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.762 CRWrnafold: 0.484 Sensitivity CentroidAlifold(20): 0.636 CRWrnafold: 0.476 Positive Predictive Value CentroidAlifold(20): 0.914 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.556 CRWrnafold: 0.395 Sensitivity IPknot: 0.486 CRWrnafold: 0.398 Positive Predictive Value IPknot: 0.637 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.697 CRWrnafold: 0.458 Sensitivity Pknots: 0.668 CRWrnafold: 0.415 Positive Predictive Value Pknots: 0.733 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	328 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.629 CRWrnafold: 0.477 Sensitivity MXScarna(seed): 0.522 CRWrnafold: 0.469 Positive Predictive Value MXScarna(seed): 0.759 CRWrnafold: 0.486 Number of pairs reference - predicted secondary structure: 328 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.723 CRWrnafold: 0.484 Sensitivity RNAalifold(20): 0.622 CRWrnafold: 0.476 Positive Predictive Value RNAalifold(20): 0.841 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.525 CRWrnafold: 0.395 Sensitivity CentroidFold: 0.459 CRWrnafold: 0.398 Positive Predictive Value CentroidFold: 0.600 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.655 CRWrnafold: 0.446 Sensitivity RNASampler(seed): 0.572 CRWrnafold: 0.425 Positive Predictive Value RNASampler(seed): 0.755 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	196 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.651 CRWrnafold: 0.453 Sensitivity Multilign(20): 0.591 CRWrnafold: 0.445 Positive Predictive Value Multilign(20): 0.718 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	324 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.605 CRWrnafold: 0.476 Sensitivity RNAalifold(seed): 0.432 CRWrnafold: 0.468 Positive Predictive Value RNAalifold(seed): 0.850 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 324 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.553 CRWrnafold: 0.379 Sensitivity RNASampler(20): 0.434 CRWrnafold: 0.383 Positive Predictive Value RNASampler(20): 0.705 CRWrnafold: 0.377 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.650 CRWrnafold: 0.484 Sensitivity MXScarna(20): 0.579 CRWrnafold: 0.476 Positive Predictive Value MXScarna(20): 0.730 CRWrnafold: 0.494 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.510 CRWrnafold: 0.395 Sensitivity Contrafold: 0.490 CRWrnafold: 0.398 Positive Predictive Value Contrafold: 0.532 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	153 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.570 CRWrnafold: 0.445 Sensitivity Murlet(20): 0.440 CRWrnafold: 0.437 Positive Predictive Value Murlet(20): 0.741 CRWrnafold: 0.453 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.471 CRWrnafold: 0.395 Sensitivity Sfold: 0.417 CRWrnafold: 0.398 Positive Predictive Value Sfold: 0.533 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.464 CRWrnafold: 0.395 Sensitivity ProbKnot: 0.458 CRWrnafold: 0.398 Positive Predictive Value ProbKnot: 0.472 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.468 CRWrnafold: 0.395 Sensitivity MaxExpect: 0.452 CRWrnafold: 0.398 Positive Predictive Value MaxExpect: 0.485 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.450 CRWrnafold: 0.414 Sensitivity McQFold: 0.440 CRWrnafold: 0.417 Positive Predictive Value McQFold: 0.461 CRWrnafold: 0.412 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.584 CRWrnafold: 0.403 Sensitivity Murlet(seed): 0.492 CRWrnafold: 0.388 Positive Predictive Value Murlet(seed): 0.694 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86109605532e-08	790 Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.439 CRWrnafold: 0.395 Sensitivity Fold: 0.441 CRWrnafold: 0.398 Positive Predictive Value Fold: 0.439 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.427 CRWrnafold: 0.395 Sensitivity PknotsRG: 0.426 CRWrnafold: 0.398 Positive Predictive Value PknotsRG: 0.428 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.433 CRWrnafold: 0.395 Sensitivity UNAFold: 0.429 CRWrnafold: 0.398 Positive Predictive Value UNAFold: 0.438 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.633 CRWrnafold: 0.438 Sensitivity TurboFold(seed): 0.562 CRWrnafold: 0.425 Positive Predictive Value TurboFold(seed): 0.716 CRWrnafold: 0.456 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.02007144414e-09	627 RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.473 CRWrnafold: 0.422 Sensitivity RNAsubopt: 0.480 CRWrnafold: 0.424 Positive Predictive Value RNAsubopt: 0.468 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	503 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.426 CRWrnafold: 0.404 Sensitivity Afold: 0.421 CRWrnafold: 0.403 Positive Predictive Value Afold: 0.432 CRWrnafold: 0.406 Number of pairs reference - predicted secondary structure: 503 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.445 CRWrnafold: 0.418 Sensitivity RNASLOpt: 0.419 CRWrnafold: 0.419 Positive Predictive Value RNASLOpt: 0.474 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	790 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.424 CRWrnafold: 0.395 Sensitivity RNAfold: 0.424 CRWrnafold: 0.398 Positive Predictive Value RNAfold: 0.425 CRWrnafold: 0.394 Number of pairs reference - predicted secondary structure: 790 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.453 CRWrnafold: 0.374 Sensitivity HotKnots: 0.445 CRWrnafold: 0.351 Positive Predictive Value HotKnots: 0.469 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: 0.508 CRWrnafold: 0.458 Sensitivity RDfolder: 0.432 CRWrnafold: 0.415 Positive Predictive Value RDfolder: 0.609 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.85233844192e-08	209 CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.482 CRWrnafold: 0.456 Sensitivity CMfinder(20): 0.310 CRWrnafold: 0.447 Positive Predictive Value CMfinder(20): 0.749 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.420 RNAshapes: 0.408 Sensitivity CRWrnafold: 0.421 RNAshapes: 0.404 Positive Predictive Value CRWrnafold: 0.421 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.484 Carnac(20): 0.466 Sensitivity CRWrnafold: 0.476 Carnac(20): 0.243 Positive Predictive Value CRWrnafold: 0.494 Carnac(20): 0.895 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold5: 0.333 Sensitivity CRWrnafold: 0.421 Vsfold5: 0.317 Positive Predictive Value CRWrnafold: 0.420 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.419 Vsfold4: 0.337 Sensitivity CRWrnafold: 0.421 Vsfold4: 0.310 Positive Predictive Value CRWrnafold: 0.420 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.390 RNAwolf: 0.302 Sensitivity CRWrnafold: 0.393 RNAwolf: 0.316 Positive Predictive Value CRWrnafold: 0.389 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.467 CMfinder(seed): 0.363 Sensitivity CRWrnafold: 0.472 CMfinder(seed): 0.184 Positive Predictive Value CRWrnafold: 0.464 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.436 Carnac(seed): 0.141 Sensitivity CRWrnafold: 0.443 Carnac(seed): 0.021 Positive Predictive Value CRWrnafold: 0.432 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.484 RSpredict(20): 0.483 Sensitivity CRWrnafold: 0.476 RSpredict(20): 0.356 Positive Predictive Value CRWrnafold: 0.494 RSpredict(20): 0.655 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 0.00353686086758	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.458 Alterna: 0.393 Sensitivity CRWrnafold: 0.415 Alterna: 0.365 Positive Predictive Value CRWrnafold: 0.518 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.443 NanoFolder: 0.174 Sensitivity CRWrnafold: 0.444 NanoFolder: 0.207 Positive Predictive Value CRWrnafold: 0.445 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.477 RSpredict(seed): 0.319 Sensitivity CRWrnafold: 0.469 RSpredict(seed): 0.159 Positive Predictive Value CRWrnafold: 0.486 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 322 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.451 Mastr(20): 0.044 Sensitivity CRWrnafold: 0.442 Mastr(20): 0.003 Positive Predictive Value CRWrnafold: 0.462 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.456 Mastr(seed): 0.041 Sensitivity CRWrnafold: 0.449 Mastr(seed): 0.003 Positive Predictive Value CRWrnafold: 0.465 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.575 CRWrnafold: 0.400 Sensitivity Multilign(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value Multilign(seed): 0.625 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.666 CRWrnafold: 0.400 Sensitivity PPfold(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value PPfold(seed): 0.833 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.411 MCFold: 0.290 Sensitivity CRWrnafold: 0.380 MCFold: 0.320 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	286 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 Carnac(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.709 Carnac(20): 0.277 Positive Predictive Value PETfold_pre2.0(seed): 0.810 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.767 Carnac(20): 0.496 Sensitivity ContextFold: 0.726 Carnac(20): 0.277 Positive Predictive Value ContextFold: 0.811 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 Carnac(20): 0.512 Sensitivity CentroidAlifold(seed): 0.647 Carnac(20): 0.289 Positive Predictive Value CentroidAlifold(seed): 0.917 Carnac(20): 0.909 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Carnac(20): 0.365 Sensitivity CentroidHomfold‑LAST: 0.552 Carnac(20): 0.155 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.741 Carnac(20): 0.365 Sensitivity TurboFold(20): 0.685 Carnac(20): 0.155 Positive Predictive Value TurboFold(20): 0.802 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 Carnac(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.681 Carnac(20): 0.277 Positive Predictive Value PETfold_pre2.0(20): 0.783 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.736 Carnac(20): 0.398 Sensitivity PPfold(20): 0.641 Carnac(20): 0.181 Positive Predictive Value PPfold(20): 0.846 Carnac(20): 0.878 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.821 Cylofold: 0.756 Sensitivity Carnac(20): 0.684 Cylofold: 0.677 Positive Predictive Value Carnac(20): 0.989 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	286 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Carnac(20): 0.496 Sensitivity CentroidAlifold(20): 0.595 Carnac(20): 0.277 Positive Predictive Value CentroidAlifold(20): 0.879 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.577 Carnac(20): 0.496 Sensitivity IPknot: 0.509 Carnac(20): 0.277 Positive Predictive Value IPknot: 0.654 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.821 Pknots: 0.723 Sensitivity Carnac(20): 0.684 Pknots: 0.632 Positive Predictive Value Carnac(20): 0.989 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	226 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 Carnac(20): 0.511 Sensitivity MXScarna(seed): 0.575 Carnac(20): 0.288 Positive Predictive Value MXScarna(seed): 0.761 Carnac(20): 0.909 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Carnac(20): 0.496 Sensitivity RNAalifold(20): 0.588 Carnac(20): 0.277 Positive Predictive Value RNAalifold(20): 0.760 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.539 Carnac(20): 0.496 Sensitivity CentroidFold: 0.474 Carnac(20): 0.277 Positive Predictive Value CentroidFold: 0.614 Carnac(20): 0.887 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	196 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.651 Carnac(20): 0.351 Sensitivity Multilign(20): 0.591 Carnac(20): 0.144 Positive Predictive Value Multilign(20): 0.718 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 Carnac(20): 0.509 Sensitivity RNAalifold(seed): 0.519 Carnac(20): 0.285 Positive Predictive Value RNAalifold(seed): 0.814 Carnac(20): 0.907 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.553 Carnac(20): 0.468 Sensitivity RNASampler(20): 0.434 Carnac(20): 0.261 Positive Predictive Value RNASampler(20): 0.705 Carnac(20): 0.838 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.608 Carnac(20): 0.496 Sensitivity MXScarna(20): 0.550 Carnac(20): 0.277 Positive Predictive Value MXScarna(20): 0.674 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.523 Carnac(20): 0.496 Sensitivity Contrafold: 0.504 Carnac(20): 0.277 Positive Predictive Value Contrafold: 0.543 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.566 Carnac(20): 0.427 Sensitivity Murlet(20): 0.445 Carnac(20): 0.211 Positive Predictive Value Murlet(20): 0.722 Carnac(20): 0.866 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.496 Sfold: 0.496 Sensitivity Carnac(20): 0.277 Sfold: 0.440 Positive Predictive Value Carnac(20): 0.888 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 0.989275719324	286 Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.496 ProbKnot: 0.473 Sensitivity Carnac(20): 0.277 ProbKnot: 0.463 Positive Predictive Value Carnac(20): 0.888 ProbKnot: 0.483 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.496 MaxExpect: 0.478 Sensitivity Carnac(20): 0.277 MaxExpect: 0.464 Positive Predictive Value Carnac(20): 0.888 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.454 Carnac(20): 0.365 Sensitivity McQFold: 0.434 Carnac(20): 0.155 Positive Predictive Value McQFold: 0.476 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): N/A Murlet(seed): N/A Sensitivity Carnac(20): N/A Murlet(seed): N/A Positive Predictive Value Carnac(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	286 Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.496 Fold: 0.445 Sensitivity Carnac(20): 0.277 Fold: 0.446 Positive Predictive Value Carnac(20): 0.888 Fold: 0.445 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.509 PknotsRG: 0.482 Sensitivity Carnac(20): 0.287 PknotsRG: 0.474 Positive Predictive Value Carnac(20): 0.904 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.496 UNAFold: 0.459 Sensitivity Carnac(20): 0.277 UNAFold: 0.454 Positive Predictive Value Carnac(20): 0.888 UNAFold: 0.465 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): N/A Carnac(20): N/A Sensitivity TurboFold(seed): N/A Carnac(20): N/A Positive Predictive Value TurboFold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	209 RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.520 Carnac(20): 0.365 Sensitivity RNAsubopt: 0.518 Carnac(20): 0.155 Positive Predictive Value RNAsubopt: 0.523 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.496 Afold: 0.453 Sensitivity Carnac(20): 0.276 Afold: 0.449 Positive Predictive Value Carnac(20): 0.893 Afold: 0.458 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.456 Carnac(20): 0.358 Sensitivity RNASLOpt: 0.421 Carnac(20): 0.150 Positive Predictive Value RNASLOpt: 0.496 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.496 RNAfold: 0.444 Sensitivity Carnac(20): 0.277 RNAfold: 0.443 Positive Predictive Value Carnac(20): 0.888 RNAfold: 0.446 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.821 HotKnots: 0.717 Sensitivity Carnac(20): 0.684 HotKnots: 0.639 Positive Predictive Value Carnac(20): 0.989 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.821 RDfolder: 0.664 Sensitivity Carnac(20): 0.684 RDfolder: 0.586 Positive Predictive Value Carnac(20): 0.989 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	209 CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.482 Carnac(20): 0.365 Sensitivity CMfinder(20): 0.310 Carnac(20): 0.155 Positive Predictive Value CMfinder(20): 0.749 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.457 Carnac(20): 0.364 Sensitivity RNAshapes: 0.442 Carnac(20): 0.154 Positive Predictive Value RNAshapes: 0.474 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.484 Carnac(20): 0.466 Sensitivity CRWrnafold: 0.476 Carnac(20): 0.243 Positive Predictive Value CRWrnafold: 0.494 Carnac(20): 0.895 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Vsfold5 vs Carnac(20) Matthews Correlation Coefficient Vsfold5: 0.371 Carnac(20): 0.364 Sensitivity Vsfold5: 0.344 Carnac(20): 0.154 Positive Predictive Value Vsfold5: 0.403 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 1.95308298399e-06	- Vsfold4 vs Carnac(20) Matthews Correlation Coefficient Vsfold4: 0.392 Carnac(20): 0.363 Sensitivity Vsfold4: 0.355 Carnac(20): 0.153 Positive Predictive Value Vsfold4: 0.436 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAwolf vs Carnac(20) Matthews Correlation Coefficient RNAwolf: 0.368 Carnac(20): 0.365 Sensitivity RNAwolf: 0.378 Carnac(20): 0.155 Positive Predictive Value RNAwolf: 0.361 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 4.28774587736e-06	? 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	? Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.563 Carnac(seed): 0.552 Sensitivity Carnac(20): 0.338 Carnac(seed): 0.327 Positive Predictive Value Carnac(20): 0.938 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.496 RSpredict(20): 0.425 Sensitivity Carnac(20): 0.277 RSpredict(20): 0.345 Positive Predictive Value Carnac(20): 0.888 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.821 Alterna: 0.656 Sensitivity Carnac(20): 0.684 Alterna: 0.602 Positive Predictive Value Carnac(20): 0.989 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.392 NanoFolder: 0.152 Sensitivity Carnac(20): 0.178 NanoFolder: 0.174 Positive Predictive Value Carnac(20): 0.863 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.507 RSpredict(seed): 0.402 Sensitivity Carnac(20): 0.282 RSpredict(seed): 0.269 Positive Predictive Value Carnac(20): 0.910 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.397 Mastr(20): 0.035 Sensitivity Carnac(20): 0.188 Mastr(20): 0.002 Positive Predictive Value Carnac(20): 0.842 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.353 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.140 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): N/A Carnac(20): N/A Sensitivity PPfold(seed): N/A Carnac(20): N/A Positive Predictive Value PPfold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.821 MCFold: 0.291 Sensitivity Carnac(20): 0.684 MCFold: 0.323 Positive Predictive Value Carnac(20): 0.989 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Vsfold5	503 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold5: 0.327 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold5: 0.310 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold5: 0.347 Number of pairs reference - predicted secondary structure: 503 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.729 Vsfold5: 0.333 Sensitivity ContextFold: 0.685 Vsfold5: 0.317 Positive Predictive Value ContextFold: 0.777 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	272 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.698 Vsfold5: 0.381 Sensitivity CentroidAlifold(seed): 0.529 Vsfold5: 0.351 Positive Predictive Value CentroidAlifold(seed): 0.922 Vsfold5: 0.416 Number of pairs reference - predicted secondary structure: 272 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Vsfold5: 0.333 Sensitivity CentroidHomfold‑LAST: 0.473 Vsfold5: 0.317 Positive Predictive Value CentroidHomfold‑LAST: 0.869 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold5: 0.371 Sensitivity TurboFold(20): 0.683 Vsfold5: 0.344 Positive Predictive Value TurboFold(20): 0.800 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Vsfold5: 0.371 Sensitivity PETfold_pre2.0(20): 0.656 Vsfold5: 0.344 Positive Predictive Value PETfold_pre2.0(20): 0.830 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	195 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.738 Vsfold5: 0.370 Sensitivity PPfold(20): 0.639 Vsfold5: 0.343 Positive Predictive Value PPfold(20): 0.852 Vsfold5: 0.402 Number of pairs reference - predicted secondary structure: 195 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.701 Vsfold5: 0.557 Sensitivity Cylofold: 0.673 Vsfold5: 0.513 Positive Predictive Value Cylofold: 0.734 Vsfold5: 0.611 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Vsfold5: 0.371 Sensitivity CentroidAlifold(20): 0.563 Vsfold5: 0.344 Positive Predictive Value CentroidAlifold(20): 0.917 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.601 Vsfold5: 0.333 Sensitivity IPknot: 0.543 Vsfold5: 0.317 Positive Predictive Value IPknot: 0.667 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.697 Vsfold5: 0.597 Sensitivity Pknots: 0.668 Vsfold5: 0.550 Positive Predictive Value Pknots: 0.733 Vsfold5: 0.657 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.603 Vsfold5: 0.382 Sensitivity MXScarna(seed): 0.485 Vsfold5: 0.352 Positive Predictive Value MXScarna(seed): 0.751 Vsfold5: 0.417 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.663 Vsfold5: 0.371 Sensitivity RNAalifold(20): 0.536 Vsfold5: 0.344 Positive Predictive Value RNAalifold(20): 0.821 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.568 Vsfold5: 0.333 Sensitivity CentroidFold: 0.512 Vsfold5: 0.317 Positive Predictive Value CentroidFold: 0.631 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold5: 0.452 Sensitivity RNASampler(seed): 0.572 Vsfold5: 0.435 Positive Predictive Value RNASampler(seed): 0.755 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	189 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.651 Vsfold5: 0.373 Sensitivity Multilign(20): 0.591 Vsfold5: 0.345 Positive Predictive Value Multilign(20): 0.717 Vsfold5: 0.405 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	273 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.468 Vsfold5: 0.381 Sensitivity RNAalifold(seed): 0.271 Vsfold5: 0.351 Positive Predictive Value RNAalifold(seed): 0.809 Vsfold5: 0.416 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.553 Vsfold5: 0.259 Sensitivity RNASampler(20): 0.434 Vsfold5: 0.248 Positive Predictive Value RNASampler(20): 0.705 Vsfold5: 0.272 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.623 Vsfold5: 0.371 Sensitivity MXScarna(20): 0.548 Vsfold5: 0.344 Positive Predictive Value MXScarna(20): 0.709 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.549 Vsfold5: 0.333 Sensitivity Contrafold: 0.535 Vsfold5: 0.317 Positive Predictive Value Contrafold: 0.565 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	144 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.555 Vsfold5: 0.354 Sensitivity Murlet(20): 0.422 Vsfold5: 0.329 Positive Predictive Value Murlet(20): 0.731 Vsfold5: 0.383 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.510 Vsfold5: 0.333 Sensitivity Sfold: 0.459 Vsfold5: 0.317 Positive Predictive Value Sfold: 0.568 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.522 Vsfold5: 0.333 Sensitivity ProbKnot: 0.516 Vsfold5: 0.317 Positive Predictive Value ProbKnot: 0.530 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.523 Vsfold5: 0.333 Sensitivity MaxExpect: 0.509 Vsfold5: 0.317 Positive Predictive Value MaxExpect: 0.539 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.460 Vsfold5: 0.333 Sensitivity McQFold: 0.449 Vsfold5: 0.317 Positive Predictive Value McQFold: 0.473 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold5: 0.452 Sensitivity Murlet(seed): 0.319 Vsfold5: 0.435 Positive Predictive Value Murlet(seed): 0.734 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.84361416392e-08	591 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.497 Vsfold5: 0.333 Sensitivity Fold: 0.498 Vsfold5: 0.317 Positive Predictive Value Fold: 0.497 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.474 Vsfold5: 0.333 Sensitivity PknotsRG: 0.475 Vsfold5: 0.317 Positive Predictive Value PknotsRG: 0.475 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.473 Vsfold5: 0.333 Sensitivity UNAFold: 0.469 Vsfold5: 0.317 Positive Predictive Value UNAFold: 0.478 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.633 Vsfold5: 0.379 Sensitivity TurboFold(seed): 0.562 Vsfold5: 0.369 Positive Predictive Value TurboFold(seed): 0.716 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.52577670387e-09	591 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.469 Vsfold5: 0.333 Sensitivity RNAsubopt: 0.475 Vsfold5: 0.317 Positive Predictive Value RNAsubopt: 0.464 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	334 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.497 Vsfold5: 0.368 Sensitivity Afold: 0.489 Vsfold5: 0.344 Positive Predictive Value Afold: 0.506 Vsfold5: 0.396 Number of pairs reference - predicted secondary structure: 334 Wilcoxon single-rank test P-value: 3.56938820447e-08	533 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold5: 0.337 Sensitivity RNASLOpt: 0.421 Vsfold5: 0.320 Positive Predictive Value RNASLOpt: 0.474 Vsfold5: 0.356 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.473 Vsfold5: 0.333 Sensitivity RNAfold: 0.473 Vsfold5: 0.317 Positive Predictive Value RNAfold: 0.474 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs HotKnots Matthews Correlation Coefficient Vsfold5: 0.534 HotKnots: 0.453 Sensitivity Vsfold5: 0.505 HotKnots: 0.445 Positive Predictive Value Vsfold5: 0.572 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.597 RDfolder: 0.508 Sensitivity Vsfold5: 0.550 RDfolder: 0.432 Positive Predictive Value Vsfold5: 0.657 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.490 Vsfold5: 0.371 Sensitivity CMfinder(20): 0.318 Vsfold5: 0.344 Positive Predictive Value CMfinder(20): 0.756 Vsfold5: 0.403 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	575 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold5: 0.335 Sensitivity RNAshapes: 0.402 Vsfold5: 0.318 Positive Predictive Value RNAshapes: 0.412 Vsfold5: 0.355 Number of pairs reference - predicted secondary structure: 575 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold5: 0.333 Sensitivity CRWrnafold: 0.421 Vsfold5: 0.317 Positive Predictive Value CRWrnafold: 0.420 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 Vsfold5 vs Carnac(20) Matthews Correlation Coefficient Vsfold5: 0.371 Carnac(20): 0.364 Sensitivity Vsfold5: 0.344 Carnac(20): 0.154 Positive Predictive Value Vsfold5: 0.403 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 1.95308298399e-06		- Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.338 Vsfold5: 0.333 Sensitivity Vsfold4: 0.311 Vsfold5: 0.317 Positive Predictive Value Vsfold4: 0.369 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.340 Vsfold5: 0.333 Sensitivity RNAwolf: 0.354 Vsfold5: 0.317 Positive Predictive Value RNAwolf: 0.328 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.372 CMfinder(seed): 0.359 Sensitivity Vsfold5: 0.348 CMfinder(seed): 0.186 Positive Predictive Value Vsfold5: 0.401 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.23414297917e-07	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.303 Carnac(seed): 0.166 Sensitivity Vsfold5: 0.289 Carnac(seed): 0.029 Positive Predictive Value Vsfold5: 0.320 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.371 RSpredict(20): 0.353 Sensitivity Vsfold5: 0.344 RSpredict(20): 0.226 Positive Predictive Value Vsfold5: 0.403 RSpredict(20): 0.555 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.597 Alterna: 0.393 Sensitivity Vsfold5: 0.550 Alterna: 0.365 Positive Predictive Value Vsfold5: 0.657 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.346 NanoFolder: 0.178 Sensitivity Vsfold5: 0.324 NanoFolder: 0.210 Positive Predictive Value Vsfold5: 0.372 NanoFolder: 0.153 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.381 RSpredict(seed): 0.059 Sensitivity Vsfold5: 0.351 RSpredict(seed): 0.015 Positive Predictive Value Vsfold5: 0.416 RSpredict(seed): 0.236 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.371 Mastr(20): 0.045 Sensitivity Vsfold5: 0.344 Mastr(20): 0.003 Positive Predictive Value Vsfold5: 0.403 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.377 Mastr(seed): 0.043 Sensitivity Vsfold5: 0.349 Mastr(seed): 0.003 Positive Predictive Value Vsfold5: 0.410 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold5: 0.423 Sensitivity Multilign(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value Multilign(seed): 0.625 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold5: 0.423 Sensitivity PPfold(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value PPfold(seed): 0.833 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.555 MCFold: 0.290 Sensitivity Vsfold5: 0.517 MCFold: 0.320 Positive Predictive Value Vsfold5: 0.604 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	509 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold4: 0.332 Sensitivity PETfold_pre2.0(seed): 0.595 Vsfold4: 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Vsfold4: 0.364 Number of pairs reference - predicted secondary structure: 509 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.726 Vsfold4: 0.337 Sensitivity ContextFold: 0.683 Vsfold4: 0.310 Positive Predictive Value ContextFold: 0.773 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	276 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.698 Vsfold4: 0.407 Sensitivity CentroidAlifold(seed): 0.529 Vsfold4: 0.367 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold4: 0.454 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Vsfold4: 0.337 Sensitivity CentroidHomfold‑LAST: 0.474 Vsfold4: 0.310 Positive Predictive Value CentroidHomfold‑LAST: 0.869 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.739 Vsfold4: 0.392 Sensitivity TurboFold(20): 0.684 Vsfold4: 0.355 Positive Predictive Value TurboFold(20): 0.800 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Vsfold4: 0.392 Sensitivity PETfold_pre2.0(20): 0.655 Vsfold4: 0.355 Positive Predictive Value PETfold_pre2.0(20): 0.830 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	198 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.737 Vsfold4: 0.392 Sensitivity PPfold(20): 0.638 Vsfold4: 0.355 Positive Predictive Value PPfold(20): 0.852 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.701 Vsfold4: 0.449 Sensitivity Cylofold: 0.673 Vsfold4: 0.395 Positive Predictive Value Cylofold: 0.734 Vsfold4: 0.517 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Vsfold4: 0.392 Sensitivity CentroidAlifold(20): 0.563 Vsfold4: 0.355 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.601 Vsfold4: 0.337 Sensitivity IPknot: 0.543 Vsfold4: 0.310 Positive Predictive Value IPknot: 0.666 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.697 Vsfold4: 0.480 Sensitivity Pknots: 0.668 Vsfold4: 0.423 Positive Predictive Value Pknots: 0.733 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	281 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.605 Vsfold4: 0.407 Sensitivity MXScarna(seed): 0.488 Vsfold4: 0.367 Positive Predictive Value MXScarna(seed): 0.752 Vsfold4: 0.454 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.662 Vsfold4: 0.392 Sensitivity RNAalifold(20): 0.535 Vsfold4: 0.355 Positive Predictive Value RNAalifold(20): 0.821 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.568 Vsfold4: 0.337 Sensitivity CentroidFold: 0.512 Vsfold4: 0.310 Positive Predictive Value CentroidFold: 0.631 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold4: 0.392 Sensitivity RNASampler(seed): 0.572 Vsfold4: 0.365 Positive Predictive Value RNASampler(seed): 0.755 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	192 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.649 Vsfold4: 0.395 Sensitivity Multilign(20): 0.590 Vsfold4: 0.357 Positive Predictive Value Multilign(20): 0.716 Vsfold4: 0.438 Number of pairs reference - predicted secondary structure: 192 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.470 Vsfold4: 0.407 Sensitivity RNAalifold(seed): 0.274 Vsfold4: 0.366 Positive Predictive Value RNAalifold(seed): 0.810 Vsfold4: 0.453 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.553 Vsfold4: 0.260 Sensitivity RNASampler(20): 0.434 Vsfold4: 0.242 Positive Predictive Value RNASampler(20): 0.705 Vsfold4: 0.281 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.626 Vsfold4: 0.392 Sensitivity MXScarna(20): 0.552 Vsfold4: 0.355 Positive Predictive Value MXScarna(20): 0.712 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.549 Vsfold4: 0.337 Sensitivity Contrafold: 0.535 Vsfold4: 0.310 Positive Predictive Value Contrafold: 0.565 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.553 Vsfold4: 0.375 Sensitivity Murlet(20): 0.420 Vsfold4: 0.340 Positive Predictive Value Murlet(20): 0.730 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.510 Vsfold4: 0.337 Sensitivity Sfold: 0.459 Vsfold4: 0.310 Positive Predictive Value Sfold: 0.568 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.521 Vsfold4: 0.337 Sensitivity ProbKnot: 0.516 Vsfold4: 0.310 Positive Predictive Value ProbKnot: 0.528 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.522 Vsfold4: 0.337 Sensitivity MaxExpect: 0.508 Vsfold4: 0.310 Positive Predictive Value MaxExpect: 0.538 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.459 Vsfold4: 0.337 Sensitivity McQFold: 0.448 Vsfold4: 0.310 Positive Predictive Value McQFold: 0.472 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold4: 0.392 Sensitivity Murlet(seed): 0.319 Vsfold4: 0.365 Positive Predictive Value Murlet(seed): 0.734 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.43573297697e-08	600 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.495 Vsfold4: 0.337 Sensitivity Fold: 0.497 Vsfold4: 0.310 Positive Predictive Value Fold: 0.496 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.475 Vsfold4: 0.337 Sensitivity PknotsRG: 0.475 Vsfold4: 0.310 Positive Predictive Value PknotsRG: 0.476 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.473 Vsfold4: 0.337 Sensitivity UNAFold: 0.469 Vsfold4: 0.310 Positive Predictive Value UNAFold: 0.478 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.633 Vsfold4: 0.257 Sensitivity TurboFold(seed): 0.562 Vsfold4: 0.240 Positive Predictive Value TurboFold(seed): 0.716 Vsfold4: 0.283 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	600 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.469 Vsfold4: 0.337 Sensitivity RNAsubopt: 0.476 Vsfold4: 0.310 Positive Predictive Value RNAsubopt: 0.464 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	340 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.495 Vsfold4: 0.377 Sensitivity Afold: 0.488 Vsfold4: 0.344 Positive Predictive Value Afold: 0.504 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	533 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold4: 0.340 Sensitivity RNASLOpt: 0.421 Vsfold4: 0.313 Positive Predictive Value RNASLOpt: 0.474 Vsfold4: 0.371 Number of pairs reference - predicted secondary structure: 533 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.474 Vsfold4: 0.337 Sensitivity RNAfold: 0.474 Vsfold4: 0.310 Positive Predictive Value RNAfold: 0.475 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.453 Vsfold4: 0.423 Sensitivity HotKnots: 0.445 Vsfold4: 0.380 Positive Predictive Value HotKnots: 0.469 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: 0.508 Vsfold4: 0.480 Sensitivity RDfolder: 0.432 Vsfold4: 0.423 Positive Predictive Value RDfolder: 0.609 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 2.63254822069e-07	204 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.488 Vsfold4: 0.392 Sensitivity CMfinder(20): 0.316 Vsfold4: 0.355 Positive Predictive Value CMfinder(20): 0.754 Vsfold4: 0.436 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	576 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold4: 0.340 Sensitivity RNAshapes: 0.402 Vsfold4: 0.313 Positive Predictive Value RNAshapes: 0.412 Vsfold4: 0.371 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.419 Vsfold4: 0.337 Sensitivity CRWrnafold: 0.421 Vsfold4: 0.310 Positive Predictive Value CRWrnafold: 0.420 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Vsfold4 vs Carnac(20) Matthews Correlation Coefficient Vsfold4: 0.392 Carnac(20): 0.363 Sensitivity Vsfold4: 0.355 Carnac(20): 0.153 Positive Predictive Value Vsfold4: 0.436 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.338 Vsfold5: 0.333 Sensitivity Vsfold4: 0.311 Vsfold5: 0.317 Positive Predictive Value Vsfold4: 0.369 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold4: 0.337 Sensitivity RNAwolf: 0.354 Vsfold4: 0.310 Positive Predictive Value RNAwolf: 0.328 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 8.67590017402e-07	+ Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.402 CMfinder(seed): 0.359 Sensitivity Vsfold4: 0.370 CMfinder(seed): 0.186 Positive Predictive Value Vsfold4: 0.439 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.317 Carnac(seed): 0.161 Sensitivity Vsfold4: 0.292 Carnac(seed): 0.027 Positive Predictive Value Vsfold4: 0.347 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.392 RSpredict(20): 0.353 Sensitivity Vsfold4: 0.355 RSpredict(20): 0.225 Positive Predictive Value Vsfold4: 0.436 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.480 Alterna: 0.393 Sensitivity Vsfold4: 0.423 Alterna: 0.365 Positive Predictive Value Vsfold4: 0.557 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.363 NanoFolder: 0.177 Sensitivity Vsfold4: 0.331 NanoFolder: 0.210 Positive Predictive Value Vsfold4: 0.400 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.407 RSpredict(seed): 0.064 Sensitivity Vsfold4: 0.367 RSpredict(seed): 0.017 Positive Predictive Value Vsfold4: 0.454 RSpredict(seed): 0.251 Number of pairs reference - predicted secondary structure: 279 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.392 Mastr(20): 0.045 Sensitivity Vsfold4: 0.355 Mastr(20): 0.003 Positive Predictive Value Vsfold4: 0.436 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.402 Mastr(seed): 0.043 Sensitivity Vsfold4: 0.363 Mastr(seed): 0.003 Positive Predictive Value Vsfold4: 0.447 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 259 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold4: 0.260 Sensitivity Multilign(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value Multilign(seed): 0.625 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold4: 0.260 Sensitivity PPfold(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value PPfold(seed): 0.833 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.435 MCFold: 0.290 Sensitivity Vsfold4: 0.387 MCFold: 0.320 Positive Predictive Value Vsfold4: 0.498 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAwolf	527 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAwolf: 0.341 Sensitivity PETfold_pre2.0(seed): 0.590 RNAwolf: 0.356 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAwolf: 0.329 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.715 RNAwolf: 0.302 Sensitivity ContextFold: 0.670 RNAwolf: 0.316 Positive Predictive Value ContextFold: 0.764 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	294 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 RNAwolf: 0.373 Sensitivity CentroidAlifold(seed): 0.522 RNAwolf: 0.382 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 294 Wilcoxon single-rank test P-value: 3.56938820447e-08	627 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.638 RNAwolf: 0.339 Sensitivity CentroidHomfold‑LAST: 0.468 RNAwolf: 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.870 RNAwolf: 0.327 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.741 RNAwolf: 0.368 Sensitivity TurboFold(20): 0.685 RNAwolf: 0.378 Positive Predictive Value TurboFold(20): 0.802 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAwolf: 0.368 Sensitivity PETfold_pre2.0(20): 0.653 RNAwolf: 0.378 Positive Predictive Value PETfold_pre2.0(20): 0.830 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.735 RNAwolf: 0.370 Sensitivity PPfold(20): 0.635 RNAwolf: 0.380 Positive Predictive Value PPfold(20): 0.851 RNAwolf: 0.362 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.701 RNAwolf: 0.389 Sensitivity Cylofold: 0.673 RNAwolf: 0.374 Positive Predictive Value Cylofold: 0.734 RNAwolf: 0.413 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.718 RNAwolf: 0.368 Sensitivity CentroidAlifold(20): 0.562 RNAwolf: 0.378 Positive Predictive Value CentroidAlifold(20): 0.917 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.567 RNAwolf: 0.302 Sensitivity IPknot: 0.499 RNAwolf: 0.316 Positive Predictive Value IPknot: 0.646 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.697 RNAwolf: 0.401 Sensitivity Pknots: 0.668 RNAwolf: 0.381 Positive Predictive Value Pknots: 0.733 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	299 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.594 RNAwolf: 0.374 Sensitivity MXScarna(seed): 0.475 RNAwolf: 0.382 Positive Predictive Value MXScarna(seed): 0.744 RNAwolf: 0.368 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.661 RNAwolf: 0.368 Sensitivity RNAalifold(20): 0.533 RNAwolf: 0.378 Positive Predictive Value RNAalifold(20): 0.820 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.542 RNAwolf: 0.302 Sensitivity CentroidFold: 0.477 RNAwolf: 0.316 Positive Predictive Value CentroidFold: 0.616 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAwolf: 0.438 Sensitivity RNASampler(seed): 0.572 RNAwolf: 0.407 Positive Predictive Value RNASampler(seed): 0.755 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.43573297697e-08	196 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.651 RNAwolf: 0.366 Sensitivity Multilign(20): 0.591 RNAwolf: 0.376 Positive Predictive Value Multilign(20): 0.718 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNAwolf: 0.373 Sensitivity RNAalifold(seed): 0.275 RNAwolf: 0.382 Positive Predictive Value RNAalifold(seed): 0.812 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.553 RNAwolf: 0.296 Sensitivity RNASampler(20): 0.434 RNAwolf: 0.315 Positive Predictive Value RNASampler(20): 0.705 RNAwolf: 0.281 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.627 RNAwolf: 0.368 Sensitivity MXScarna(20): 0.553 RNAwolf: 0.378 Positive Predictive Value MXScarna(20): 0.713 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.527 RNAwolf: 0.302 Sensitivity Contrafold: 0.506 RNAwolf: 0.316 Positive Predictive Value Contrafold: 0.549 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.550 RNAwolf: 0.355 Sensitivity Murlet(20): 0.416 RNAwolf: 0.367 Positive Predictive Value Murlet(20): 0.727 RNAwolf: 0.345 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.484 RNAwolf: 0.302 Sensitivity Sfold: 0.430 RNAwolf: 0.316 Positive Predictive Value Sfold: 0.546 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.488 RNAwolf: 0.302 Sensitivity ProbKnot: 0.482 RNAwolf: 0.316 Positive Predictive Value ProbKnot: 0.495 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.491 RNAwolf: 0.302 Sensitivity MaxExpect: 0.474 RNAwolf: 0.316 Positive Predictive Value MaxExpect: 0.510 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	669 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.450 RNAwolf: 0.329 Sensitivity McQFold: 0.440 RNAwolf: 0.344 Positive Predictive Value McQFold: 0.461 RNAwolf: 0.317 Number of pairs reference - predicted secondary structure: 669 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.482 RNAwolf: 0.438 Sensitivity Murlet(seed): 0.319 RNAwolf: 0.407 Positive Predictive Value Murlet(seed): 0.734 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.26434400251e-08	740 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.461 RNAwolf: 0.302 Sensitivity Fold: 0.462 RNAwolf: 0.316 Positive Predictive Value Fold: 0.461 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.446 RNAwolf: 0.302 Sensitivity PknotsRG: 0.445 RNAwolf: 0.316 Positive Predictive Value PknotsRG: 0.447 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.445 RNAwolf: 0.302 Sensitivity UNAFold: 0.440 RNAwolf: 0.316 Positive Predictive Value UNAFold: 0.450 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.633 RNAwolf: 0.497 Sensitivity TurboFold(seed): 0.562 RNAwolf: 0.481 Positive Predictive Value TurboFold(seed): 0.716 RNAwolf: 0.519 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	627 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.473 RNAwolf: 0.339 Sensitivity RNAsubopt: 0.480 RNAwolf: 0.354 Positive Predictive Value RNAsubopt: 0.468 RNAwolf: 0.327 Number of pairs reference - predicted secondary structure: 627 Wilcoxon single-rank test P-value: 3.56938820447e-08	457 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.446 RNAwolf: 0.301 Sensitivity Afold: 0.439 RNAwolf: 0.312 Positive Predictive Value Afold: 0.453 RNAwolf: 0.292 Number of pairs reference - predicted secondary structure: 457 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.445 RNAwolf: 0.336 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.351 Positive Predictive Value RNASLOpt: 0.474 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.441 RNAwolf: 0.302 Sensitivity RNAfold: 0.441 RNAwolf: 0.316 Positive Predictive Value RNAfold: 0.443 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.453 RNAwolf: 0.362 Sensitivity HotKnots: 0.445 RNAwolf: 0.353 Positive Predictive Value HotKnots: 0.469 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: 0.508 RNAwolf: 0.401 Sensitivity RDfolder: 0.432 RNAwolf: 0.381 Positive Predictive Value RDfolder: 0.609 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.482 RNAwolf: 0.368 Sensitivity CMfinder(20): 0.310 RNAwolf: 0.378 Positive Predictive Value CMfinder(20): 0.749 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	579 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.408 RNAwolf: 0.341 Sensitivity RNAshapes: 0.404 RNAwolf: 0.355 Positive Predictive Value RNAshapes: 0.414 RNAwolf: 0.329 Number of pairs reference - predicted secondary structure: 579 Wilcoxon single-rank test P-value: 3.56938820447e-08	740 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.390 RNAwolf: 0.302 Sensitivity CRWrnafold: 0.393 RNAwolf: 0.316 Positive Predictive Value CRWrnafold: 0.389 RNAwolf: 0.289 Number of pairs reference - predicted secondary structure: 740 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAwolf vs Carnac(20) Matthews Correlation Coefficient RNAwolf: 0.368 Carnac(20): 0.365 Sensitivity RNAwolf: 0.378 Carnac(20): 0.155 Positive Predictive Value RNAwolf: 0.361 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 4.28774587736e-06	591 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.340 Vsfold5: 0.333 Sensitivity RNAwolf: 0.354 Vsfold5: 0.317 Positive Predictive Value RNAwolf: 0.328 Vsfold5: 0.353 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	600 RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold4: 0.337 Sensitivity RNAwolf: 0.354 Vsfold4: 0.310 Positive Predictive Value RNAwolf: 0.328 Vsfold4: 0.368 Number of pairs reference - predicted secondary structure: 600 Wilcoxon single-rank test P-value: 8.67590017402e-07		- CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.363 RNAwolf: 0.262 Sensitivity CMfinder(seed): 0.184 RNAwolf: 0.270 Positive Predictive Value CMfinder(seed): 0.716 RNAwolf: 0.257 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.298 Carnac(seed): 0.141 Sensitivity RNAwolf: 0.312 Carnac(seed): 0.021 Positive Predictive Value RNAwolf: 0.287 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(20) Matthews Correlation Coefficient RNAwolf: 0.368 RSpredict(20): 0.350 Sensitivity RNAwolf: 0.378 RSpredict(20): 0.222 Positive Predictive Value RNAwolf: 0.361 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.401 Alterna: 0.393 Sensitivity RNAwolf: 0.381 Alterna: 0.365 Positive Predictive Value RNAwolf: 0.434 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00114276330813	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.337 NanoFolder: 0.174 Sensitivity RNAwolf: 0.349 NanoFolder: 0.207 Positive Predictive Value RNAwolf: 0.327 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.373 RSpredict(seed): 0.064 Sensitivity RNAwolf: 0.381 RSpredict(seed): 0.017 Positive Predictive Value RNAwolf: 0.367 RSpredict(seed): 0.248 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.368 Mastr(20): 0.044 Sensitivity RNAwolf: 0.378 Mastr(20): 0.003 Positive Predictive Value RNAwolf: 0.361 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.370 Mastr(seed): 0.041 Sensitivity RNAwolf: 0.379 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.363 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.575 RNAwolf: 0.455 Sensitivity Multilign(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value Multilign(seed): 0.625 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.666 RNAwolf: 0.455 Sensitivity PPfold(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value PPfold(seed): 0.833 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.376 MCFold: 0.290 Sensitivity RNAwolf: 0.364 MCFold: 0.320 Positive Predictive Value RNAwolf: 0.400 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	26 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.457 CMfinder(seed): 0.363 Sensitivity PETfold_pre2.0(seed): 0.309 CMfinder(seed): 0.184 Positive Predictive Value PETfold_pre2.0(seed): 0.678 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.678 CMfinder(seed): 0.363 Sensitivity ContextFold: 0.632 CMfinder(seed): 0.184 Positive Predictive Value ContextFold: 0.729 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.473 CMfinder(seed): 0.363 Sensitivity CentroidAlifold(seed): 0.295 CMfinder(seed): 0.184 Positive Predictive Value CentroidAlifold(seed): 0.759 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.651 CMfinder(seed): 0.363 Sensitivity CentroidHomfold‑LAST: 0.493 CMfinder(seed): 0.184 Positive Predictive Value CentroidHomfold‑LAST: 0.860 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	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 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	9 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: 0.797 CMfinder(seed): 0.439 Sensitivity Cylofold: 0.801 CMfinder(seed): 0.348 Positive Predictive Value Cylofold: 0.797 CMfinder(seed): 0.563 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	26 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.623 CMfinder(seed): 0.363 Sensitivity IPknot: 0.563 CMfinder(seed): 0.184 Positive Predictive Value IPknot: 0.690 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	10 Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: 0.767 CMfinder(seed): 0.459 Sensitivity Pknots: 0.787 CMfinder(seed): 0.365 Positive Predictive Value Pknots: 0.752 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	26 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 MXScarna(seed): 0.307 Sensitivity CMfinder(seed): 0.184 MXScarna(seed): 0.199 Positive Predictive Value CMfinder(seed): 0.716 MXScarna(seed): 0.476 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	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	26 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.599 CMfinder(seed): 0.363 Sensitivity CentroidFold: 0.525 CMfinder(seed): 0.184 Positive Predictive Value CentroidFold: 0.684 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	11 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 CMfinder(seed): 0.443 Sensitivity RNASampler(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value RNASampler(seed): 0.753 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.26710183075e-09	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	26 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.450 CMfinder(seed): 0.363 Sensitivity RNAalifold(seed): 0.255 CMfinder(seed): 0.184 Positive Predictive Value RNAalifold(seed): 0.798 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	0 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs 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	26 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.577 CMfinder(seed): 0.363 Sensitivity Contrafold: 0.554 CMfinder(seed): 0.184 Positive Predictive Value Contrafold: 0.602 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	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	26 Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.580 CMfinder(seed): 0.363 Sensitivity Sfold: 0.515 CMfinder(seed): 0.184 Positive Predictive Value Sfold: 0.653 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.549 CMfinder(seed): 0.363 Sensitivity ProbKnot: 0.542 CMfinder(seed): 0.184 Positive Predictive Value ProbKnot: 0.557 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.552 CMfinder(seed): 0.363 Sensitivity MaxExpect: 0.535 CMfinder(seed): 0.184 Positive Predictive Value MaxExpect: 0.571 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.526 CMfinder(seed): 0.363 Sensitivity McQFold: 0.510 CMfinder(seed): 0.184 Positive Predictive Value McQFold: 0.544 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.488 CMfinder(seed): 0.443 Sensitivity Murlet(seed): 0.321 CMfinder(seed): 0.333 Positive Predictive Value Murlet(seed): 0.748 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.18293266588e-07	26 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.505 CMfinder(seed): 0.363 Sensitivity Fold: 0.507 CMfinder(seed): 0.184 Positive Predictive Value Fold: 0.505 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.544 CMfinder(seed): 0.363 Sensitivity PknotsRG: 0.551 CMfinder(seed): 0.184 Positive Predictive Value PknotsRG: 0.539 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.485 CMfinder(seed): 0.363 Sensitivity UNAFold: 0.476 CMfinder(seed): 0.184 Positive Predictive Value UNAFold: 0.495 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	7 CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.589 TurboFold(seed): 0.569 Sensitivity CMfinder(seed): 0.455 TurboFold(seed): 0.508 Positive Predictive Value CMfinder(seed): 0.769 TurboFold(seed): 0.644 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	26 RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.490 CMfinder(seed): 0.363 Sensitivity RNAsubopt: 0.496 CMfinder(seed): 0.184 Positive Predictive Value RNAsubopt: 0.486 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.522 CMfinder(seed): 0.355 Sensitivity Afold: 0.512 CMfinder(seed): 0.182 Positive Predictive Value Afold: 0.533 CMfinder(seed): 0.696 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 CMfinder(seed): 0.373 Sensitivity RNASLOpt: 0.443 CMfinder(seed): 0.200 Positive Predictive Value RNASLOpt: 0.510 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	26 RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.466 CMfinder(seed): 0.363 Sensitivity RNAfold: 0.466 CMfinder(seed): 0.184 Positive Predictive Value RNAfold: 0.468 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: 0.456 CMfinder(seed): 0.443 Sensitivity HotKnots: 0.458 CMfinder(seed): 0.333 Positive Predictive Value HotKnots: 0.462 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00972644458282	10 RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: 0.538 CMfinder(seed): 0.459 Sensitivity RDfolder: 0.472 CMfinder(seed): 0.365 Positive Predictive Value RDfolder: 0.620 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	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	24 RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.540 CMfinder(seed): 0.359 Sensitivity RNAshapes: 0.531 CMfinder(seed): 0.186 Positive Predictive Value RNAshapes: 0.550 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.467 CMfinder(seed): 0.363 Sensitivity CRWrnafold: 0.472 CMfinder(seed): 0.184 Positive Predictive Value CRWrnafold: 0.464 CMfinder(seed): 0.716 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	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	24 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.372 CMfinder(seed): 0.359 Sensitivity Vsfold5: 0.348 CMfinder(seed): 0.186 Positive Predictive Value Vsfold5: 0.401 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.23414297917e-07	24 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.402 CMfinder(seed): 0.359 Sensitivity Vsfold4: 0.370 CMfinder(seed): 0.186 Positive Predictive Value Vsfold4: 0.439 CMfinder(seed): 0.698 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.363 RNAwolf: 0.262 Sensitivity CMfinder(seed): 0.184 RNAwolf: 0.270 Positive Predictive Value CMfinder(seed): 0.716 RNAwolf: 0.257 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 Carnac(seed): 0.212 Sensitivity CMfinder(seed): 0.184 Carnac(seed): 0.047 Positive Predictive Value CMfinder(seed): 0.716 Carnac(seed): 0.953 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.459 Alterna: 0.360 Sensitivity CMfinder(seed): 0.365 Alterna: 0.345 Positive Predictive Value CMfinder(seed): 0.585 Alterna: 0.386 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.08932646657e-08	? CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.307 NanoFolder: 0.236 Sensitivity CMfinder(seed): 0.139 NanoFolder: 0.279 Positive Predictive Value CMfinder(seed): 0.679 NanoFolder: 0.202 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 RSpredict(seed): 0.187 Sensitivity CMfinder(seed): 0.184 RSpredict(seed): 0.067 Positive Predictive Value CMfinder(seed): 0.716 RSpredict(seed): 0.523 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 Mastr(seed): 0.132 Sensitivity CMfinder(seed): 0.184 Mastr(seed): 0.029 Positive Predictive Value CMfinder(seed): 0.716 Mastr(seed): 0.602 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.562 CMfinder(seed): 0.553 Sensitivity Multilign(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value Multilign(seed): 0.604 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.662 CMfinder(seed): 0.553 Sensitivity PPfold(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value PPfold(seed): 0.833 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.499 MCFold: 0.352 Sensitivity CMfinder(seed): 0.385 MCFold: 0.408 Positive Predictive Value CMfinder(seed): 0.657 MCFold: 0.315 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
Carnac(seed)	62 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.654 Carnac(seed): 0.253 Sensitivity PETfold_pre2.0(seed): 0.534 Carnac(seed): 0.068 Positive Predictive Value PETfold_pre2.0(seed): 0.802 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.677 Carnac(seed): 0.253 Sensitivity ContextFold: 0.640 Carnac(seed): 0.068 Positive Predictive Value ContextFold: 0.716 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.680 Carnac(seed): 0.253 Sensitivity CentroidAlifold(seed): 0.514 Carnac(seed): 0.068 Positive Predictive Value CentroidAlifold(seed): 0.899 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.632 Carnac(seed): 0.146 Sensitivity CentroidHomfold‑LAST: 0.466 Carnac(seed): 0.022 Positive Predictive Value CentroidHomfold‑LAST: 0.858 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.781 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.777 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.786 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.860 Carnac(seed): 0.552 Sensitivity PETfold_pre2.0(20): 0.830 Carnac(seed): 0.327 Positive Predictive Value PETfold_pre2.0(20): 0.891 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.818 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.738 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.907 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	11 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.831 Carnac(seed): 0.550 Sensitivity Cylofold: 0.834 Carnac(seed): 0.313 Positive Predictive Value Cylofold: 0.830 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	4 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.897 Carnac(seed): 0.552 Sensitivity CentroidAlifold(20): 0.852 Carnac(seed): 0.327 Positive Predictive Value CentroidAlifold(20): 0.945 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	62 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.588 Carnac(seed): 0.253 Sensitivity IPknot: 0.539 Carnac(seed): 0.068 Positive Predictive Value IPknot: 0.643 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.803 Carnac(seed): 0.531 Sensitivity Pknots: 0.820 Carnac(seed): 0.292 Positive Predictive Value Pknots: 0.789 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.95953827463e-09	62 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.533 Carnac(seed): 0.253 Sensitivity MXScarna(seed): 0.405 Carnac(seed): 0.068 Positive Predictive Value MXScarna(seed): 0.703 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.807 Carnac(seed): 0.552 Sensitivity RNAalifold(20): 0.745 Carnac(seed): 0.327 Positive Predictive Value RNAalifold(20): 0.874 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	62 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.589 Carnac(seed): 0.253 Sensitivity CentroidFold: 0.540 Carnac(seed): 0.068 Positive Predictive Value CentroidFold: 0.643 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Carnac(seed): 0.582 Sensitivity RNASampler(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value RNASampler(seed): 0.755 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	2 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.644 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.662 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	62 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Carnac(seed): 0.253 Sensitivity RNAalifold(seed): 0.465 Carnac(seed): 0.068 Positive Predictive Value RNAalifold(seed): 0.894 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): N/A Carnac(seed): N/A Sensitivity RNASampler(20): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.776 Carnac(seed): 0.552 Sensitivity MXScarna(20): 0.752 Carnac(seed): 0.327 Positive Predictive Value MXScarna(20): 0.800 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	62 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.568 Carnac(seed): 0.253 Sensitivity Contrafold: 0.557 Carnac(seed): 0.068 Positive Predictive Value Contrafold: 0.579 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.333 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.243 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.456 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	62 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.564 Carnac(seed): 0.253 Sensitivity Sfold: 0.509 Carnac(seed): 0.068 Positive Predictive Value Sfold: 0.625 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.529 Carnac(seed): 0.253 Sensitivity ProbKnot: 0.523 Carnac(seed): 0.068 Positive Predictive Value ProbKnot: 0.535 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.533 Carnac(seed): 0.253 Sensitivity MaxExpect: 0.524 Carnac(seed): 0.068 Positive Predictive Value MaxExpect: 0.543 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.473 Carnac(seed): 0.141 Sensitivity McQFold: 0.465 Carnac(seed): 0.021 Positive Predictive Value McQFold: 0.482 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs Murlet(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Murlet(seed): 0.482 Sensitivity Carnac(seed): 0.354 Murlet(seed): 0.319 Positive Predictive Value Carnac(seed): 0.962 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.52299983238e-08	62 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.494 Carnac(seed): 0.253 Sensitivity Fold: 0.497 Carnac(seed): 0.068 Positive Predictive Value Fold: 0.491 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.529 Carnac(seed): 0.253 Sensitivity PknotsRG: 0.533 Carnac(seed): 0.068 Positive Predictive Value PknotsRG: 0.526 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.511 Carnac(seed): 0.253 Sensitivity UNAFold: 0.508 Carnac(seed): 0.068 Positive Predictive Value UNAFold: 0.514 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 Carnac(seed): 0.485 Sensitivity TurboFold(seed): 0.562 Carnac(seed): 0.245 Positive Predictive Value TurboFold(seed): 0.716 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71210682542e-09	57 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.487 Carnac(seed): 0.146 Sensitivity RNAsubopt: 0.495 Carnac(seed): 0.022 Positive Predictive Value RNAsubopt: 0.481 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.501 Carnac(seed): 0.259 Sensitivity Afold: 0.499 Carnac(seed): 0.071 Positive Predictive Value Afold: 0.503 Carnac(seed): 0.937 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Carnac(seed): 0.178 Sensitivity RNASLOpt: 0.425 Carnac(seed): 0.033 Positive Predictive Value RNASLOpt: 0.503 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.501 Carnac(seed): 0.253 Sensitivity RNAfold: 0.503 Carnac(seed): 0.068 Positive Predictive Value RNAfold: 0.500 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs HotKnots Matthews Correlation Coefficient Carnac(seed): 0.582 HotKnots: 0.522 Sensitivity Carnac(seed): 0.354 HotKnots: 0.526 Positive Predictive Value Carnac(seed): 0.962 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	12 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.561 Carnac(seed): 0.531 Sensitivity RDfolder: 0.481 Carnac(seed): 0.292 Positive Predictive Value RDfolder: 0.663 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.85159322687e-07	3 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.140 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.085 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.232 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	47 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.467 Carnac(seed): 0.169 Sensitivity RNAshapes: 0.458 Carnac(seed): 0.030 Positive Predictive Value RNAshapes: 0.478 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.436 Carnac(seed): 0.141 Sensitivity CRWrnafold: 0.443 Carnac(seed): 0.021 Positive Predictive Value CRWrnafold: 0.432 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.563 Carnac(seed): 0.552 Sensitivity Carnac(20): 0.338 Carnac(seed): 0.327 Positive Predictive Value Carnac(20): 0.938 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	48 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.303 Carnac(seed): 0.166 Sensitivity Vsfold5: 0.289 Carnac(seed): 0.029 Positive Predictive Value Vsfold5: 0.320 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.317 Carnac(seed): 0.161 Sensitivity Vsfold4: 0.292 Carnac(seed): 0.027 Positive Predictive Value Vsfold4: 0.347 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.298 Carnac(seed): 0.141 Sensitivity RNAwolf: 0.312 Carnac(seed): 0.021 Positive Predictive Value RNAwolf: 0.287 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 Carnac(seed): 0.212 Sensitivity CMfinder(seed): 0.184 Carnac(seed): 0.047 Positive Predictive Value CMfinder(seed): 0.716 Carnac(seed): 0.953 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08		? RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.665 Carnac(seed): 0.552 Sensitivity RSpredict(20): 0.574 Carnac(seed): 0.327 Positive Predictive Value RSpredict(20): 0.770 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Carnac(seed) vs Alterna Matthews Correlation Coefficient Carnac(seed): 0.531 Alterna: 0.384 Sensitivity Carnac(seed): 0.292 Alterna: 0.365 Positive Predictive Value Carnac(seed): 0.971 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.28439804626e-08	? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.275 Carnac(seed): 0.152 Sensitivity NanoFolder: 0.323 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.236 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= Carnac(seed) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(seed): 0.253 RSpredict(seed): 0.251 Sensitivity Carnac(seed): 0.068 RSpredict(seed): 0.102 Positive Predictive Value Carnac(seed): 0.940 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 0.476224075459	? Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.141 Mastr(seed): 0.097 Sensitivity Carnac(seed): 0.021 Mastr(seed): 0.014 Positive Predictive Value Carnac(seed): 0.962 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.625 Multilign(seed): 0.575 Sensitivity Carnac(seed): 0.407 Multilign(seed): 0.536 Positive Predictive Value Carnac(seed): 0.966 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Carnac(seed): 0.625 Sensitivity PPfold(seed): 0.536 Carnac(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): 0.566 MCFold: 0.354 Sensitivity Carnac(seed): 0.332 MCFold: 0.415 Positive Predictive Value Carnac(seed): 0.971 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.70361883708e-09
RSpredict(20)	286 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.758 RSpredict(20): 0.425 Sensitivity PETfold_pre2.0(seed): 0.709 RSpredict(20): 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.810 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.767 RSpredict(20): 0.425 Sensitivity ContextFold: 0.726 RSpredict(20): 0.345 Positive Predictive Value ContextFold: 0.811 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.770 RSpredict(20): 0.500 Sensitivity CentroidAlifold(seed): 0.647 RSpredict(20): 0.393 Positive Predictive Value CentroidAlifold(seed): 0.917 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 RSpredict(20): 0.350 Sensitivity CentroidHomfold‑LAST: 0.552 RSpredict(20): 0.222 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.741 RSpredict(20): 0.350 Sensitivity TurboFold(20): 0.685 RSpredict(20): 0.222 Positive Predictive Value TurboFold(20): 0.802 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.730 RSpredict(20): 0.425 Sensitivity PETfold_pre2.0(20): 0.681 RSpredict(20): 0.345 Positive Predictive Value PETfold_pre2.0(20): 0.783 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.736 RSpredict(20): 0.374 Sensitivity PPfold(20): 0.641 RSpredict(20): 0.252 Positive Predictive Value PPfold(20): 0.846 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.756 RSpredict(20): 0.672 Sensitivity Cylofold: 0.677 RSpredict(20): 0.549 Positive Predictive Value Cylofold: 0.849 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	286 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.723 RSpredict(20): 0.425 Sensitivity CentroidAlifold(20): 0.595 RSpredict(20): 0.345 Positive Predictive Value CentroidAlifold(20): 0.879 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.577 RSpredict(20): 0.425 Sensitivity IPknot: 0.509 RSpredict(20): 0.345 Positive Predictive Value IPknot: 0.654 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.723 RSpredict(20): 0.672 Sensitivity Pknots: 0.632 RSpredict(20): 0.549 Positive Predictive Value Pknots: 0.832 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	226 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 RSpredict(20): 0.498 Sensitivity MXScarna(seed): 0.575 RSpredict(20): 0.391 Positive Predictive Value MXScarna(seed): 0.761 RSpredict(20): 0.635 Number of pairs reference - predicted secondary structure: 226 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(20): 0.425 Sensitivity RNAalifold(20): 0.588 RSpredict(20): 0.345 Positive Predictive Value RNAalifold(20): 0.760 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.539 RSpredict(20): 0.429 Sensitivity CentroidFold: 0.474 RSpredict(20): 0.348 Positive Predictive Value CentroidFold: 0.614 RSpredict(20): 0.530 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	196 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.651 RSpredict(20): 0.335 Sensitivity Multilign(20): 0.591 RSpredict(20): 0.210 Positive Predictive Value Multilign(20): 0.718 RSpredict(20): 0.537 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.650 RSpredict(20): 0.480 Sensitivity RNAalifold(seed): 0.519 RSpredict(20): 0.380 Positive Predictive Value RNAalifold(seed): 0.814 RSpredict(20): 0.607 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.553 RSpredict(20): 0.482 Sensitivity RNASampler(20): 0.434 RSpredict(20): 0.410 Positive Predictive Value RNASampler(20): 0.705 RSpredict(20): 0.569 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.608 RSpredict(20): 0.425 Sensitivity MXScarna(20): 0.550 RSpredict(20): 0.345 Positive Predictive Value MXScarna(20): 0.674 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.523 RSpredict(20): 0.425 Sensitivity Contrafold: 0.504 RSpredict(20): 0.345 Positive Predictive Value Contrafold: 0.543 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.566 RSpredict(20): 0.402 Sensitivity Murlet(20): 0.445 RSpredict(20): 0.292 Positive Predictive Value Murlet(20): 0.722 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.496 RSpredict(20): 0.425 Sensitivity Sfold: 0.440 RSpredict(20): 0.345 Positive Predictive Value Sfold: 0.559 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.473 RSpredict(20): 0.425 Sensitivity ProbKnot: 0.463 RSpredict(20): 0.345 Positive Predictive Value ProbKnot: 0.483 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.478 RSpredict(20): 0.425 Sensitivity MaxExpect: 0.464 RSpredict(20): 0.345 Positive Predictive Value MaxExpect: 0.492 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.454 RSpredict(20): 0.350 Sensitivity McQFold: 0.434 RSpredict(20): 0.222 Positive Predictive Value McQFold: 0.476 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): N/A Murlet(seed): N/A Sensitivity RSpredict(20): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	286 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.445 RSpredict(20): 0.425 Sensitivity Fold: 0.446 RSpredict(20): 0.345 Positive Predictive Value Fold: 0.445 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.539 PknotsRG: 0.482 Sensitivity RSpredict(20): 0.421 PknotsRG: 0.474 Positive Predictive Value RSpredict(20): 0.690 PknotsRG: 0.490 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.459 RSpredict(20): 0.425 Sensitivity UNAFold: 0.454 RSpredict(20): 0.345 Positive Predictive Value UNAFold: 0.465 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RSpredict(20) vs TurboFold(seed) Matthews Correlation Coefficient RSpredict(20): N/A TurboFold(seed): N/A Sensitivity RSpredict(20): N/A TurboFold(seed): N/A Positive Predictive Value RSpredict(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	209 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.520 RSpredict(20): 0.350 Sensitivity RNAsubopt: 0.518 RSpredict(20): 0.222 Positive Predictive Value RNAsubopt: 0.523 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.453 RSpredict(20): 0.417 Sensitivity Afold: 0.449 RSpredict(20): 0.338 Positive Predictive Value Afold: 0.458 RSpredict(20): 0.515 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.456 RSpredict(20): 0.355 Sensitivity RNASLOpt: 0.421 RSpredict(20): 0.227 Positive Predictive Value RNASLOpt: 0.496 RSpredict(20): 0.557 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	286 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.444 RSpredict(20): 0.425 Sensitivity RNAfold: 0.443 RSpredict(20): 0.345 Positive Predictive Value RNAfold: 0.446 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.717 RSpredict(20): 0.672 Sensitivity HotKnots: 0.639 RSpredict(20): 0.549 Positive Predictive Value HotKnots: 0.810 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.672 RDfolder: 0.664 Sensitivity RSpredict(20): 0.549 RDfolder: 0.586 Positive Predictive Value RSpredict(20): 0.830 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	209 CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.482 RSpredict(20): 0.350 Sensitivity CMfinder(20): 0.310 RSpredict(20): 0.222 Positive Predictive Value CMfinder(20): 0.749 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.457 RSpredict(20): 0.355 Sensitivity RNAshapes: 0.442 RSpredict(20): 0.226 Positive Predictive Value RNAshapes: 0.474 RSpredict(20): 0.558 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.484 RSpredict(20): 0.483 Sensitivity CRWrnafold: 0.476 RSpredict(20): 0.356 Positive Predictive Value CRWrnafold: 0.494 RSpredict(20): 0.655 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 0.00353686086758	286 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.496 RSpredict(20): 0.425 Sensitivity Carnac(20): 0.277 RSpredict(20): 0.345 Positive Predictive Value Carnac(20): 0.888 RSpredict(20): 0.524 Number of pairs reference - predicted secondary structure: 286 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.371 RSpredict(20): 0.353 Sensitivity Vsfold5: 0.344 RSpredict(20): 0.226 Positive Predictive Value Vsfold5: 0.403 RSpredict(20): 0.555 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.392 RSpredict(20): 0.353 Sensitivity Vsfold4: 0.355 RSpredict(20): 0.225 Positive Predictive Value Vsfold4: 0.436 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAwolf vs RSpredict(20) Matthews Correlation Coefficient RNAwolf: 0.368 RSpredict(20): 0.350 Sensitivity RNAwolf: 0.378 RSpredict(20): 0.222 Positive Predictive Value RNAwolf: 0.361 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	4 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.665 Carnac(seed): 0.552 Sensitivity RSpredict(20): 0.574 Carnac(seed): 0.327 Positive Predictive Value RSpredict(20): 0.770 Carnac(seed): 0.932 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.672 Alterna: 0.656 Sensitivity RSpredict(20): 0.549 Alterna: 0.602 Positive Predictive Value RSpredict(20): 0.830 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.354 NanoFolder: 0.152 Sensitivity RSpredict(20): 0.223 NanoFolder: 0.174 Positive Predictive Value RSpredict(20): 0.564 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 RSpredict(seed): 0.402 Sensitivity RSpredict(20): 0.381 RSpredict(seed): 0.269 Positive Predictive Value RSpredict(20): 0.628 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.236 Mastr(20): 0.035 Sensitivity RSpredict(20): 0.177 Mastr(20): 0.002 Positive Predictive Value RSpredict(20): 0.317 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.292 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.173 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.494 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): N/A PPfold(seed): N/A Sensitivity RSpredict(20): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.672 MCFold: 0.291 Sensitivity RSpredict(20): 0.549 MCFold: 0.323 Positive Predictive Value RSpredict(20): 0.830 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Alterna	18 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Alterna: 0.503 Sensitivity PETfold_pre2.0(seed): 0.661 Alterna: 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.823 Alterna: 0.543 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.22210847902e-08	46 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.500 Alterna: 0.393 Sensitivity ContextFold: 0.441 Alterna: 0.365 Positive Predictive Value ContextFold: 0.577 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Alterna: 0.486 Sensitivity CentroidAlifold(seed): 0.642 Alterna: 0.455 Positive Predictive Value CentroidAlifold(seed): 0.936 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.39162260866e-08	46 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 Alterna: 0.393 Sensitivity CentroidHomfold‑LAST: 0.471 Alterna: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.857 Alterna: 0.656 Sensitivity TurboFold(20): 0.744 Alterna: 0.602 Positive Predictive Value TurboFold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Alterna: 0.656 Sensitivity PETfold_pre2.0(20): 0.759 Alterna: 0.602 Positive Predictive Value PETfold_pre2.0(20): 0.962 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.840 Alterna: 0.656 Sensitivity PPfold(20): 0.737 Alterna: 0.602 Positive Predictive Value PPfold(20): 0.961 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	45 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.764 Alterna: 0.401 Sensitivity Cylofold: 0.742 Alterna: 0.372 Positive Predictive Value Cylofold: 0.791 Alterna: 0.446 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Alterna: 0.656 Sensitivity CentroidAlifold(20): 0.752 Alterna: 0.602 Positive Predictive Value CentroidAlifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.558 Alterna: 0.393 Sensitivity IPknot: 0.501 Alterna: 0.365 Positive Predictive Value IPknot: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.697 Alterna: 0.393 Sensitivity Pknots: 0.668 Alterna: 0.365 Positive Predictive Value Pknots: 0.733 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.514 Alterna: 0.486 Sensitivity MXScarna(seed): 0.481 Alterna: 0.455 Positive Predictive Value MXScarna(seed): 0.558 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.47710327474e-08	5 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.844 Alterna: 0.656 Sensitivity RNAalifold(20): 0.722 Alterna: 0.602 Positive Predictive Value RNAalifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.544 Alterna: 0.393 Sensitivity CentroidFold: 0.485 Alterna: 0.365 Positive Predictive Value CentroidFold: 0.621 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.641 Alterna: 0.384 Sensitivity RNASampler(seed): 0.562 Alterna: 0.365 Positive Predictive Value RNASampler(seed): 0.736 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	5 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.862 Alterna: 0.656 Sensitivity Multilign(20): 0.752 Alterna: 0.602 Positive Predictive Value Multilign(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	16 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.651 Alterna: 0.486 Sensitivity RNAalifold(seed): 0.519 Alterna: 0.455 Positive Predictive Value RNAalifold(seed): 0.823 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	5 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.840 Alterna: 0.656 Sensitivity RNASampler(20): 0.714 Alterna: 0.602 Positive Predictive Value RNASampler(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.837 Alterna: 0.656 Sensitivity MXScarna(20): 0.752 Alterna: 0.602 Positive Predictive Value MXScarna(20): 0.935 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.515 Alterna: 0.393 Sensitivity Contrafold: 0.477 Alterna: 0.365 Positive Predictive Value Contrafold: 0.567 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.741 Alterna: 0.656 Sensitivity Murlet(20): 0.594 Alterna: 0.602 Positive Predictive Value Murlet(20): 0.929 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.482 Alterna: 0.393 Sensitivity Sfold: 0.435 Alterna: 0.365 Positive Predictive Value Sfold: 0.545 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.527 Alterna: 0.393 Sensitivity ProbKnot: 0.496 Alterna: 0.365 Positive Predictive Value ProbKnot: 0.570 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.503 Alterna: 0.393 Sensitivity MaxExpect: 0.463 Alterna: 0.365 Positive Predictive Value MaxExpect: 0.559 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.705 Alterna: 0.393 Sensitivity McQFold: 0.679 Alterna: 0.365 Positive Predictive Value McQFold: 0.738 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Murlet(seed) vs Alterna Matthews Correlation Coefficient Murlet(seed): 0.432 Alterna: 0.384 Sensitivity Murlet(seed): 0.283 Alterna: 0.365 Positive Predictive Value Murlet(seed): 0.667 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.2940533826e-08	46 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.504 Alterna: 0.393 Sensitivity Fold: 0.466 Alterna: 0.365 Positive Predictive Value Fold: 0.556 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.627 Alterna: 0.393 Sensitivity PknotsRG: 0.601 Alterna: 0.365 Positive Predictive Value PknotsRG: 0.662 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.468 Alterna: 0.393 Sensitivity UNAFold: 0.431 Alterna: 0.365 Positive Predictive Value UNAFold: 0.521 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.600 Alterna: 0.428 Sensitivity TurboFold(seed): 0.518 Alterna: 0.399 Positive Predictive Value TurboFold(seed): 0.702 Alterna: 0.469 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	46 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.470 Alterna: 0.393 Sensitivity RNAsubopt: 0.435 Alterna: 0.365 Positive Predictive Value RNAsubopt: 0.520 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Alterna vs Afold Matthews Correlation Coefficient Alterna: 0.340 Afold: 0.309 Sensitivity Alterna: 0.326 Afold: 0.296 Positive Predictive Value Alterna: 0.369 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	46 RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.549 Alterna: 0.393 Sensitivity RNASLOpt: 0.489 Alterna: 0.365 Positive Predictive Value RNASLOpt: 0.626 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.476 Alterna: 0.393 Sensitivity RNAfold: 0.439 Alterna: 0.365 Positive Predictive Value RNAfold: 0.528 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.534 Alterna: 0.393 Sensitivity HotKnots: 0.510 Alterna: 0.365 Positive Predictive Value HotKnots: 0.569 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: 0.508 Alterna: 0.393 Sensitivity RDfolder: 0.432 Alterna: 0.365 Positive Predictive Value RDfolder: 0.609 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.779 Alterna: 0.656 Sensitivity CMfinder(20): 0.617 Alterna: 0.602 Positive Predictive Value CMfinder(20): 0.988 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.463 Alterna: 0.393 Sensitivity RNAshapes: 0.426 Alterna: 0.365 Positive Predictive Value RNAshapes: 0.515 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.458 Alterna: 0.393 Sensitivity CRWrnafold: 0.415 Alterna: 0.365 Positive Predictive Value CRWrnafold: 0.518 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.821 Alterna: 0.656 Sensitivity Carnac(20): 0.684 Alterna: 0.602 Positive Predictive Value Carnac(20): 0.989 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	46 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.597 Alterna: 0.393 Sensitivity Vsfold5: 0.550 Alterna: 0.365 Positive Predictive Value Vsfold5: 0.657 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.480 Alterna: 0.393 Sensitivity Vsfold4: 0.423 Alterna: 0.365 Positive Predictive Value Vsfold4: 0.557 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.401 Alterna: 0.393 Sensitivity RNAwolf: 0.381 Alterna: 0.365 Positive Predictive Value RNAwolf: 0.434 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00114276330813	10 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.459 Alterna: 0.360 Sensitivity CMfinder(seed): 0.365 Alterna: 0.345 Positive Predictive Value CMfinder(seed): 0.585 Alterna: 0.386 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.08932646657e-08	12 Carnac(seed) vs Alterna Matthews Correlation Coefficient Carnac(seed): 0.531 Alterna: 0.384 Sensitivity Carnac(seed): 0.292 Alterna: 0.365 Positive Predictive Value Carnac(seed): 0.971 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.28439804626e-08	5 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.672 Alterna: 0.656 Sensitivity RSpredict(20): 0.549 Alterna: 0.602 Positive Predictive Value RSpredict(20): 0.830 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.435 NanoFolder: 0.304 Sensitivity Alterna: 0.404 NanoFolder: 0.343 Positive Predictive Value Alterna: 0.479 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): 0.518 Alterna: 0.486 Sensitivity RSpredict(seed): 0.437 Alterna: 0.455 Positive Predictive Value RSpredict(seed): 0.623 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.6764152501e-07	? Alterna vs Mastr(20) Matthews Correlation Coefficient Alterna: 0.656 Mastr(20): 0.561 Sensitivity Alterna: 0.602 Mastr(20): 0.459 Positive Predictive Value Alterna: 0.721 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.486 Mastr(seed): 0.365 Sensitivity Alterna: 0.455 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.529 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	? Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.575 Alterna: 0.414 Sensitivity Multilign(seed): 0.536 Alterna: 0.386 Positive Predictive Value Multilign(seed): 0.625 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): 0.666 Alterna: 0.414 Sensitivity PPfold(seed): 0.536 Alterna: 0.386 Positive Predictive Value PPfold(seed): 0.833 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.399 MCFold: 0.296 Sensitivity Alterna: 0.369 MCFold: 0.325 Positive Predictive Value Alterna: 0.444 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
NanoFolder	97 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.692 NanoFolder: 0.178 Sensitivity PETfold_pre2.0(seed): 0.598 NanoFolder: 0.210 Positive Predictive Value PETfold_pre2.0(seed): 0.801 NanoFolder: 0.153 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.756 NanoFolder: 0.174 Sensitivity ContextFold: 0.712 NanoFolder: 0.207 Positive Predictive Value ContextFold: 0.804 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 NanoFolder: 0.184 Sensitivity CentroidAlifold(seed): 0.514 NanoFolder: 0.210 Positive Predictive Value CentroidAlifold(seed): 0.913 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	110 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 NanoFolder: 0.176 Sensitivity CentroidHomfold‑LAST: 0.480 NanoFolder: 0.209 Positive Predictive Value CentroidHomfold‑LAST: 0.876 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.729 NanoFolder: 0.152 Sensitivity TurboFold(20): 0.674 NanoFolder: 0.174 Positive Predictive Value TurboFold(20): 0.789 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 NanoFolder: 0.152 Sensitivity PETfold_pre2.0(20): 0.650 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.831 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.734 NanoFolder: 0.155 Sensitivity PPfold(20): 0.633 NanoFolder: 0.178 Positive Predictive Value PPfold(20): 0.850 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.663 NanoFolder: 0.191 Sensitivity Cylofold: 0.602 NanoFolder: 0.218 Positive Predictive Value Cylofold: 0.734 NanoFolder: 0.175 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	51 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.713 NanoFolder: 0.152 Sensitivity CentroidAlifold(20): 0.562 NanoFolder: 0.174 Positive Predictive Value CentroidAlifold(20): 0.906 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.628 NanoFolder: 0.174 Sensitivity IPknot: 0.565 NanoFolder: 0.207 Positive Predictive Value IPknot: 0.700 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.808 NanoFolder: 0.304 Sensitivity Pknots: 0.759 NanoFolder: 0.343 Positive Predictive Value Pknots: 0.863 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	60 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.586 NanoFolder: 0.184 Sensitivity MXScarna(seed): 0.470 NanoFolder: 0.210 Positive Predictive Value MXScarna(seed): 0.731 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.660 NanoFolder: 0.152 Sensitivity RNAalifold(20): 0.538 NanoFolder: 0.174 Positive Predictive Value RNAalifold(20): 0.811 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.585 NanoFolder: 0.174 Sensitivity CentroidFold: 0.527 NanoFolder: 0.207 Positive Predictive Value CentroidFold: 0.652 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 NanoFolder vs RNASampler(seed) Matthews Correlation Coefficient NanoFolder: 0.585 RNASampler(seed): 0.559 Sensitivity NanoFolder: 0.654 RNASampler(seed): 0.481 Positive Predictive Value NanoFolder: 0.531 RNASampler(seed): 0.658 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	46 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.635 NanoFolder: 0.159 Sensitivity Multilign(20): 0.579 NanoFolder: 0.182 Positive Predictive Value Multilign(20): 0.699 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	60 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.457 NanoFolder: 0.184 Sensitivity RNAalifold(seed): 0.261 NanoFolder: 0.210 Positive Predictive Value RNAalifold(seed): 0.802 NanoFolder: 0.164 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.634 NanoFolder: 0.100 Sensitivity RNASampler(20): 0.523 NanoFolder: 0.123 Positive Predictive Value RNASampler(20): 0.771 NanoFolder: 0.084 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	51 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.631 NanoFolder: 0.152 Sensitivity MXScarna(20): 0.556 NanoFolder: 0.174 Positive Predictive Value MXScarna(20): 0.718 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.565 NanoFolder: 0.174 Sensitivity Contrafold: 0.549 NanoFolder: 0.207 Positive Predictive Value Contrafold: 0.582 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.541 NanoFolder: 0.151 Sensitivity Murlet(20): 0.405 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.725 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.539 NanoFolder: 0.174 Sensitivity Sfold: 0.482 NanoFolder: 0.207 Positive Predictive Value Sfold: 0.604 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.548 NanoFolder: 0.174 Sensitivity ProbKnot: 0.540 NanoFolder: 0.207 Positive Predictive Value ProbKnot: 0.558 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.549 NanoFolder: 0.174 Sensitivity MaxExpect: 0.532 NanoFolder: 0.207 Positive Predictive Value MaxExpect: 0.569 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.448 NanoFolder: 0.174 Sensitivity McQFold: 0.436 NanoFolder: 0.207 Positive Predictive Value McQFold: 0.463 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Murlet(seed): 0.574 Sensitivity NanoFolder: 0.654 Murlet(seed): 0.423 Positive Predictive Value NanoFolder: 0.531 Murlet(seed): 0.786 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	112 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.511 NanoFolder: 0.174 Sensitivity Fold: 0.511 NanoFolder: 0.207 Positive Predictive Value Fold: 0.513 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.491 NanoFolder: 0.174 Sensitivity PknotsRG: 0.490 NanoFolder: 0.207 Positive Predictive Value PknotsRG: 0.493 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.498 NanoFolder: 0.174 Sensitivity UNAFold: 0.492 NanoFolder: 0.207 Positive Predictive Value UNAFold: 0.506 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.709 NanoFolder: 0.585 Sensitivity TurboFold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value TurboFold(seed): 0.906 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	110 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.504 NanoFolder: 0.176 Sensitivity RNAsubopt: 0.509 NanoFolder: 0.209 Positive Predictive Value RNAsubopt: 0.501 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.524 NanoFolder: 0.172 Sensitivity Afold: 0.514 NanoFolder: 0.199 Positive Predictive Value Afold: 0.535 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.464 NanoFolder: 0.181 Sensitivity RNASLOpt: 0.432 NanoFolder: 0.212 Positive Predictive Value RNASLOpt: 0.501 NanoFolder: 0.157 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.493 NanoFolder: 0.174 Sensitivity RNAfold: 0.491 NanoFolder: 0.207 Positive Predictive Value RNAfold: 0.497 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.431 NanoFolder: 0.304 Sensitivity HotKnots: 0.416 NanoFolder: 0.343 Positive Predictive Value HotKnots: 0.457 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.466 NanoFolder: 0.304 Sensitivity RDfolder: 0.398 NanoFolder: 0.343 Positive Predictive Value RDfolder: 0.555 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	51 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.487 NanoFolder: 0.152 Sensitivity CMfinder(20): 0.310 NanoFolder: 0.174 Positive Predictive Value CMfinder(20): 0.766 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.434 NanoFolder: 0.177 Sensitivity RNAshapes: 0.426 NanoFolder: 0.209 Positive Predictive Value RNAshapes: 0.444 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.443 NanoFolder: 0.174 Sensitivity CRWrnafold: 0.444 NanoFolder: 0.207 Positive Predictive Value CRWrnafold: 0.445 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.392 NanoFolder: 0.152 Sensitivity Carnac(20): 0.178 NanoFolder: 0.174 Positive Predictive Value Carnac(20): 0.863 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	107 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.346 NanoFolder: 0.178 Sensitivity Vsfold5: 0.324 NanoFolder: 0.210 Positive Predictive Value Vsfold5: 0.372 NanoFolder: 0.153 Number of pairs reference - predicted secondary structure: 107 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.363 NanoFolder: 0.177 Sensitivity Vsfold4: 0.331 NanoFolder: 0.210 Positive Predictive Value Vsfold4: 0.400 NanoFolder: 0.152 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.337 NanoFolder: 0.174 Sensitivity RNAwolf: 0.349 NanoFolder: 0.207 Positive Predictive Value RNAwolf: 0.327 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.307 NanoFolder: 0.236 Sensitivity CMfinder(seed): 0.139 NanoFolder: 0.279 Positive Predictive Value CMfinder(seed): 0.679 NanoFolder: 0.202 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.275 Carnac(seed): 0.152 Sensitivity NanoFolder: 0.323 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.236 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	51 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.354 NanoFolder: 0.152 Sensitivity RSpredict(20): 0.223 NanoFolder: 0.174 Positive Predictive Value RSpredict(20): 0.564 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.435 NanoFolder: 0.304 Sensitivity Alterna: 0.404 NanoFolder: 0.343 Positive Predictive Value Alterna: 0.479 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		+ NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.184 RSpredict(seed): 0.050 Sensitivity NanoFolder: 0.210 RSpredict(seed): 0.013 Positive Predictive Value NanoFolder: 0.164 RSpredict(seed): 0.195 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.152 Mastr(20): 0.046 Sensitivity NanoFolder: 0.174 Mastr(20): 0.004 Positive Predictive Value NanoFolder: 0.135 Mastr(20): 0.525 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.183 Mastr(seed): 0.040 Sensitivity NanoFolder: 0.209 Mastr(seed): 0.003 Positive Predictive Value NanoFolder: 0.163 Mastr(seed): 0.500 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.618 NanoFolder: 0.585 Sensitivity Multilign(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value Multilign(seed): 0.690 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.698 NanoFolder: 0.585 Sensitivity PPfold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value PPfold(seed): 0.879 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.304 MCFold: 0.248 Sensitivity NanoFolder: 0.343 MCFold: 0.283 Positive Predictive Value NanoFolder: 0.281 MCFold: 0.229 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
RSpredict(seed)	354 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.760 RSpredict(seed): 0.363 Sensitivity PETfold_pre2.0(seed): 0.700 RSpredict(seed): 0.222 Positive Predictive Value PETfold_pre2.0(seed): 0.826 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.814 RSpredict(seed): 0.363 Sensitivity ContextFold: 0.768 RSpredict(seed): 0.222 Positive Predictive Value ContextFold: 0.863 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	351 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 RSpredict(seed): 0.364 Sensitivity CentroidAlifold(seed): 0.610 RSpredict(seed): 0.223 Positive Predictive Value CentroidAlifold(seed): 0.908 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 351 Wilcoxon single-rank test P-value: 3.56938820447e-08	293 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RSpredict(seed): 0.065 Sensitivity CentroidHomfold‑LAST: 0.509 RSpredict(seed): 0.017 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(seed): 0.254 Number of pairs reference - predicted secondary structure: 293 Wilcoxon single-rank test P-value: 3.56938820447e-08	168 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RSpredict(seed): 0.063 Sensitivity TurboFold(20): 0.703 RSpredict(seed): 0.016 Positive Predictive Value TurboFold(20): 0.824 RSpredict(seed): 0.246 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	220 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.771 RSpredict(seed): 0.402 Sensitivity PETfold_pre2.0(20): 0.719 RSpredict(seed): 0.269 Positive Predictive Value PETfold_pre2.0(20): 0.826 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	165 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.760 RSpredict(seed): 0.191 Sensitivity PPfold(20): 0.669 RSpredict(seed): 0.070 Positive Predictive Value PPfold(20): 0.865 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 165 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.798 RSpredict(seed): 0.514 Sensitivity Cylofold: 0.772 RSpredict(seed): 0.434 Positive Predictive Value Cylofold: 0.828 RSpredict(seed): 0.618 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	220 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.761 RSpredict(seed): 0.402 Sensitivity CentroidAlifold(20): 0.638 RSpredict(seed): 0.269 Positive Predictive Value CentroidAlifold(20): 0.907 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.609 RSpredict(seed): 0.363 Sensitivity IPknot: 0.535 RSpredict(seed): 0.222 Positive Predictive Value IPknot: 0.694 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.768 RSpredict(seed): 0.518 Sensitivity Pknots: 0.748 RSpredict(seed): 0.437 Positive Predictive Value Pknots: 0.792 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.71568867205e-08	353 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.627 RSpredict(seed): 0.364 Sensitivity MXScarna(seed): 0.531 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.741 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	220 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.715 RSpredict(seed): 0.402 Sensitivity RNAalifold(20): 0.629 RSpredict(seed): 0.269 Positive Predictive Value RNAalifold(20): 0.814 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	353 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.576 RSpredict(seed): 0.368 Sensitivity CentroidFold: 0.506 RSpredict(seed): 0.224 Positive Predictive Value CentroidFold: 0.656 RSpredict(seed): 0.607 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RSpredict(seed): 0.488 Sensitivity RNASampler(seed): 0.572 RSpredict(seed): 0.425 Positive Predictive Value RNASampler(seed): 0.755 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	158 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.659 RSpredict(seed): 0.066 Sensitivity Multilign(20): 0.595 RSpredict(seed): 0.017 Positive Predictive Value Multilign(20): 0.730 RSpredict(seed): 0.260 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	352 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.627 RSpredict(seed): 0.364 Sensitivity RNAalifold(seed): 0.477 RSpredict(seed): 0.222 Positive Predictive Value RNAalifold(seed): 0.826 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 352 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 RSpredict(seed): 0.166 Sensitivity RNASampler(20): 0.384 RSpredict(seed): 0.052 Positive Predictive Value RNASampler(20): 0.723 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.55268413083e-08	220 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.648 RSpredict(seed): 0.402 Sensitivity MXScarna(20): 0.579 RSpredict(seed): 0.269 Positive Predictive Value MXScarna(20): 0.725 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.559 RSpredict(seed): 0.363 Sensitivity Contrafold: 0.534 RSpredict(seed): 0.222 Positive Predictive Value Contrafold: 0.585 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.560 RSpredict(seed): 0.224 Sensitivity Murlet(20): 0.430 RSpredict(seed): 0.104 Positive Predictive Value Murlet(20): 0.729 RSpredict(seed): 0.486 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.535 RSpredict(seed): 0.363 Sensitivity Sfold: 0.474 RSpredict(seed): 0.222 Positive Predictive Value Sfold: 0.605 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.512 RSpredict(seed): 0.363 Sensitivity ProbKnot: 0.498 RSpredict(seed): 0.222 Positive Predictive Value ProbKnot: 0.528 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.516 RSpredict(seed): 0.363 Sensitivity MaxExpect: 0.497 RSpredict(seed): 0.222 Positive Predictive Value MaxExpect: 0.535 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	297 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.484 RSpredict(seed): 0.064 Sensitivity McQFold: 0.463 RSpredict(seed): 0.017 Positive Predictive Value McQFold: 0.508 RSpredict(seed): 0.248 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.584 RSpredict(seed): 0.510 Sensitivity Murlet(seed): 0.492 RSpredict(seed): 0.414 Positive Predictive Value Murlet(seed): 0.694 RSpredict(seed): 0.627 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.2348692827e-08	354 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.483 RSpredict(seed): 0.363 Sensitivity Fold: 0.479 RSpredict(seed): 0.222 Positive Predictive Value Fold: 0.487 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	342 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.493 RSpredict(seed): 0.398 Sensitivity PknotsRG: 0.485 RSpredict(seed): 0.233 Positive Predictive Value PknotsRG: 0.502 RSpredict(seed): 0.681 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.498 RSpredict(seed): 0.363 Sensitivity UNAFold: 0.488 RSpredict(seed): 0.222 Positive Predictive Value UNAFold: 0.509 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 RSpredict(seed): 0.396 Sensitivity TurboFold(seed): 0.562 RSpredict(seed): 0.309 Positive Predictive Value TurboFold(seed): 0.716 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.12417824077e-10	293 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 RSpredict(seed): 0.065 Sensitivity RNAsubopt: 0.531 RSpredict(seed): 0.017 Positive Predictive Value RNAsubopt: 0.539 RSpredict(seed): 0.254 Number of pairs reference - predicted secondary structure: 293 Wilcoxon single-rank test P-value: 3.56938820447e-08	302 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.485 RSpredict(seed): 0.382 Sensitivity Afold: 0.476 RSpredict(seed): 0.240 Positive Predictive Value Afold: 0.495 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 302 Wilcoxon single-rank test P-value: 3.56938820447e-08	248 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.478 RSpredict(seed): 0.061 Sensitivity RNASLOpt: 0.440 RSpredict(seed): 0.015 Positive Predictive Value RNASLOpt: 0.521 RSpredict(seed): 0.244 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.480 RSpredict(seed): 0.363 Sensitivity RNAfold: 0.473 RSpredict(seed): 0.222 Positive Predictive Value RNAfold: 0.487 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.603 RSpredict(seed): 0.514 Sensitivity HotKnots: 0.588 RSpredict(seed): 0.427 Positive Predictive Value HotKnots: 0.624 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	16 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.616 RSpredict(seed): 0.518 Sensitivity RDfolder: 0.531 RSpredict(seed): 0.437 Positive Predictive Value RDfolder: 0.721 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.66715895098e-08	168 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.506 RSpredict(seed): 0.063 Sensitivity CMfinder(20): 0.333 RSpredict(seed): 0.016 Positive Predictive Value CMfinder(20): 0.771 RSpredict(seed): 0.246 Number of pairs reference - predicted secondary structure: 168 Wilcoxon single-rank test P-value: 3.56938820447e-08	273 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.486 RSpredict(seed): 0.060 Sensitivity RNAshapes: 0.469 RSpredict(seed): 0.015 Positive Predictive Value RNAshapes: 0.505 RSpredict(seed): 0.238 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	322 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.477 RSpredict(seed): 0.319 Sensitivity CRWrnafold: 0.469 RSpredict(seed): 0.159 Positive Predictive Value CRWrnafold: 0.486 RSpredict(seed): 0.639 Number of pairs reference - predicted secondary structure: 322 Wilcoxon single-rank test P-value: 3.56938820447e-08	220 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.507 RSpredict(seed): 0.402 Sensitivity Carnac(20): 0.282 RSpredict(seed): 0.269 Positive Predictive Value Carnac(20): 0.910 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.381 RSpredict(seed): 0.059 Sensitivity Vsfold5: 0.351 RSpredict(seed): 0.015 Positive Predictive Value Vsfold5: 0.416 RSpredict(seed): 0.236 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	279 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.407 RSpredict(seed): 0.064 Sensitivity Vsfold4: 0.367 RSpredict(seed): 0.017 Positive Predictive Value Vsfold4: 0.454 RSpredict(seed): 0.251 Number of pairs reference - predicted secondary structure: 279 Wilcoxon single-rank test P-value: 3.56938820447e-08	297 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.373 RSpredict(seed): 0.064 Sensitivity RNAwolf: 0.381 RSpredict(seed): 0.017 Positive Predictive Value RNAwolf: 0.367 RSpredict(seed): 0.248 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 RSpredict(seed): 0.187 Sensitivity CMfinder(seed): 0.184 RSpredict(seed): 0.067 Positive Predictive Value CMfinder(seed): 0.716 RSpredict(seed): 0.523 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	62 Carnac(seed) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(seed): 0.253 RSpredict(seed): 0.251 Sensitivity Carnac(seed): 0.068 RSpredict(seed): 0.102 Positive Predictive Value Carnac(seed): 0.940 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 0.476224075459	220 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 RSpredict(seed): 0.402 Sensitivity RSpredict(20): 0.381 RSpredict(seed): 0.269 Positive Predictive Value RSpredict(20): 0.628 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): 0.518 Alterna: 0.486 Sensitivity RSpredict(seed): 0.437 Alterna: 0.455 Positive Predictive Value RSpredict(seed): 0.623 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.6764152501e-07	60 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.184 RSpredict(seed): 0.050 Sensitivity NanoFolder: 0.210 RSpredict(seed): 0.013 Positive Predictive Value NanoFolder: 0.164 RSpredict(seed): 0.195 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.050 RSpredict(seed): 0.032 Sensitivity Mastr(20): 0.003 RSpredict(seed): 0.013 Positive Predictive Value Mastr(20): 0.884 RSpredict(seed): 0.080 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.056 Mastr(seed): 0.041 Sensitivity RSpredict(seed): 0.017 Mastr(seed): 0.003 Positive Predictive Value RSpredict(seed): 0.187 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 272 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RSpredict(seed): 0.437 Sensitivity Multilign(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value Multilign(seed): 0.625 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RSpredict(seed): 0.437 Sensitivity PPfold(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): 0.522 MCFold: 0.358 Sensitivity RSpredict(seed): 0.441 MCFold: 0.409 Positive Predictive Value RSpredict(seed): 0.627 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.12262428713e-08
Mastr(20)	236 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 Mastr(20): 0.035 Sensitivity PETfold_pre2.0(seed): 0.649 Mastr(20): 0.002 Positive Predictive Value PETfold_pre2.0(seed): 0.777 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.694 Mastr(20): 0.035 Sensitivity ContextFold: 0.654 Mastr(20): 0.002 Positive Predictive Value ContextFold: 0.736 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	175 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.689 Mastr(20): 0.050 Sensitivity CentroidAlifold(seed): 0.517 Mastr(20): 0.003 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Mastr(20): 0.044 Sensitivity CentroidHomfold‑LAST: 0.552 Mastr(20): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.741 Mastr(20): 0.044 Sensitivity TurboFold(20): 0.685 Mastr(20): 0.003 Positive Predictive Value TurboFold(20): 0.802 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.670 Mastr(20): 0.035 Sensitivity PETfold_pre2.0(20): 0.607 Mastr(20): 0.002 Positive Predictive Value PETfold_pre2.0(20): 0.739 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.728 Mastr(20): 0.044 Sensitivity PPfold(20): 0.630 Mastr(20): 0.003 Positive Predictive Value PPfold(20): 0.843 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.756 Mastr(20): 0.561 Sensitivity Cylofold: 0.677 Mastr(20): 0.459 Positive Predictive Value Cylofold: 0.849 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	236 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.646 Mastr(20): 0.035 Sensitivity CentroidAlifold(20): 0.493 Mastr(20): 0.002 Positive Predictive Value CentroidAlifold(20): 0.847 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.549 Mastr(20): 0.035 Sensitivity IPknot: 0.485 Mastr(20): 0.002 Positive Predictive Value IPknot: 0.622 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.723 Mastr(20): 0.561 Sensitivity Pknots: 0.632 Mastr(20): 0.459 Positive Predictive Value Pknots: 0.832 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	177 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.616 Mastr(20): 0.049 Sensitivity MXScarna(seed): 0.522 Mastr(20): 0.003 Positive Predictive Value MXScarna(seed): 0.728 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 177 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.571 Mastr(20): 0.035 Sensitivity RNAalifold(20): 0.478 Mastr(20): 0.002 Positive Predictive Value RNAalifold(20): 0.683 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.531 Mastr(20): 0.035 Sensitivity CentroidFold: 0.469 Mastr(20): 0.002 Positive Predictive Value CentroidFold: 0.601 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	196 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.651 Mastr(20): 0.046 Sensitivity Multilign(20): 0.591 Mastr(20): 0.003 Positive Predictive Value Multilign(20): 0.718 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	178 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.444 Mastr(20): 0.048 Sensitivity RNAalifold(seed): 0.285 Mastr(20): 0.003 Positive Predictive Value RNAalifold(seed): 0.692 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.553 Mastr(20): 0.096 Sensitivity RNASampler(20): 0.434 Mastr(20): 0.013 Positive Predictive Value RNASampler(20): 0.705 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.559 Mastr(20): 0.035 Sensitivity MXScarna(20): 0.503 Mastr(20): 0.002 Positive Predictive Value MXScarna(20): 0.621 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.513 Mastr(20): 0.035 Sensitivity Contrafold: 0.495 Mastr(20): 0.002 Positive Predictive Value Contrafold: 0.531 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.537 Mastr(20): 0.051 Sensitivity Murlet(20): 0.408 Mastr(20): 0.004 Positive Predictive Value Murlet(20): 0.708 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.479 Mastr(20): 0.035 Sensitivity Sfold: 0.424 Mastr(20): 0.002 Positive Predictive Value Sfold: 0.540 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.479 Mastr(20): 0.035 Sensitivity ProbKnot: 0.471 Mastr(20): 0.002 Positive Predictive Value ProbKnot: 0.487 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.483 Mastr(20): 0.035 Sensitivity MaxExpect: 0.469 Mastr(20): 0.002 Positive Predictive Value MaxExpect: 0.497 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.454 Mastr(20): 0.044 Sensitivity McQFold: 0.434 Mastr(20): 0.003 Positive Predictive Value McQFold: 0.476 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): N/A Murlet(seed): N/A Sensitivity Mastr(20): N/A Murlet(seed): N/A Positive Predictive Value Mastr(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	236 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.451 Mastr(20): 0.035 Sensitivity Fold: 0.453 Mastr(20): 0.002 Positive Predictive Value Fold: 0.450 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	210 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.508 Mastr(20): 0.044 Sensitivity PknotsRG: 0.499 Mastr(20): 0.003 Positive Predictive Value PknotsRG: 0.519 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.438 Mastr(20): 0.035 Sensitivity UNAFold: 0.435 Mastr(20): 0.002 Positive Predictive Value UNAFold: 0.442 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): N/A Mastr(20): N/A Sensitivity TurboFold(seed): N/A Mastr(20): N/A Positive Predictive Value TurboFold(seed): N/A Mastr(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	209 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.520 Mastr(20): 0.044 Sensitivity RNAsubopt: 0.518 Mastr(20): 0.003 Positive Predictive Value RNAsubopt: 0.523 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	180 Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.440 Mastr(20): 0.030 Sensitivity Afold: 0.437 Mastr(20): 0.001 Positive Predictive Value Afold: 0.442 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 180 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.456 Mastr(20): 0.047 Sensitivity RNASLOpt: 0.421 Mastr(20): 0.003 Positive Predictive Value RNASLOpt: 0.496 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.439 Mastr(20): 0.035 Sensitivity RNAfold: 0.439 Mastr(20): 0.002 Positive Predictive Value RNAfold: 0.439 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.717 Mastr(20): 0.561 Sensitivity HotKnots: 0.639 Mastr(20): 0.459 Positive Predictive Value HotKnots: 0.810 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RDfolder vs Mastr(20) Matthews Correlation Coefficient RDfolder: 0.664 Mastr(20): 0.561 Sensitivity RDfolder: 0.586 Mastr(20): 0.459 Positive Predictive Value RDfolder: 0.757 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	209 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.482 Mastr(20): 0.044 Sensitivity CMfinder(20): 0.310 Mastr(20): 0.003 Positive Predictive Value CMfinder(20): 0.749 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.457 Mastr(20): 0.046 Sensitivity RNAshapes: 0.442 Mastr(20): 0.003 Positive Predictive Value RNAshapes: 0.474 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	210 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.451 Mastr(20): 0.044 Sensitivity CRWrnafold: 0.442 Mastr(20): 0.003 Positive Predictive Value CRWrnafold: 0.462 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.397 Mastr(20): 0.035 Sensitivity Carnac(20): 0.188 Mastr(20): 0.002 Positive Predictive Value Carnac(20): 0.842 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.371 Mastr(20): 0.045 Sensitivity Vsfold5: 0.344 Mastr(20): 0.003 Positive Predictive Value Vsfold5: 0.403 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.392 Mastr(20): 0.045 Sensitivity Vsfold4: 0.355 Mastr(20): 0.003 Positive Predictive Value Vsfold4: 0.436 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.368 Mastr(20): 0.044 Sensitivity RNAwolf: 0.378 Mastr(20): 0.003 Positive Predictive Value RNAwolf: 0.361 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	3 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	236 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.236 Mastr(20): 0.035 Sensitivity RSpredict(20): 0.177 Mastr(20): 0.002 Positive Predictive Value RSpredict(20): 0.317 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Alterna vs Mastr(20) Matthews Correlation Coefficient Alterna: 0.656 Mastr(20): 0.561 Sensitivity Alterna: 0.602 Mastr(20): 0.459 Positive Predictive Value Alterna: 0.721 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	51 NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.152 Mastr(20): 0.046 Sensitivity NanoFolder: 0.174 Mastr(20): 0.004 Positive Predictive Value NanoFolder: 0.135 Mastr(20): 0.525 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.050 RSpredict(seed): 0.032 Sensitivity Mastr(20): 0.003 RSpredict(seed): 0.013 Positive Predictive Value Mastr(20): 0.884 RSpredict(seed): 0.080 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.057 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.004 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.884 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): N/A PPfold(seed): N/A Sensitivity Mastr(20): N/A PPfold(seed): N/A Positive Predictive Value Mastr(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.561 MCFold: 0.291 Sensitivity Mastr(20): 0.459 MCFold: 0.323 Positive Predictive Value Mastr(20): 0.693 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	278 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.714 Mastr(seed): 0.040 Sensitivity PETfold_pre2.0(seed): 0.629 Mastr(seed): 0.002 Positive Predictive Value PETfold_pre2.0(seed): 0.812 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.790 Mastr(seed): 0.040 Sensitivity ContextFold: 0.744 Mastr(seed): 0.002 Positive Predictive Value ContextFold: 0.839 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	270 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Mastr(seed): 0.041 Sensitivity CentroidAlifold(seed): 0.513 Mastr(seed): 0.003 Positive Predictive Value CentroidAlifold(seed): 0.910 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 270 Wilcoxon single-rank test P-value: 3.56938820447e-08	271 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Mastr(seed): 0.042 Sensitivity CentroidHomfold‑LAST: 0.511 Mastr(seed): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.761 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.823 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.668 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.755 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.661 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.864 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.798 Mastr(seed): 0.406 Sensitivity Cylofold: 0.772 Mastr(seed): 0.212 Positive Predictive Value Cylofold: 0.828 Mastr(seed): 0.784 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	154 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.555 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.925 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.629 Mastr(seed): 0.040 Sensitivity IPknot: 0.557 Mastr(seed): 0.002 Positive Predictive Value IPknot: 0.711 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.768 Mastr(seed): 0.365 Sensitivity Pknots: 0.748 Mastr(seed): 0.202 Positive Predictive Value Pknots: 0.792 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.96907987703e-08	275 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.582 Mastr(seed): 0.041 Sensitivity MXScarna(seed): 0.469 Mastr(seed): 0.002 Positive Predictive Value MXScarna(seed): 0.723 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.653 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.526 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.811 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.614 Mastr(seed): 0.041 Sensitivity CentroidFold: 0.548 Mastr(seed): 0.002 Positive Predictive Value CentroidFold: 0.689 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Mastr(seed): 0.400 Sensitivity RNASampler(seed): 0.572 Mastr(seed): 0.242 Positive Predictive Value RNASampler(seed): 0.755 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.98760236454e-08	142 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.661 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.599 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.731 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 142 Wilcoxon single-rank test P-value: 3.56938820447e-08	271 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.472 Mastr(seed): 0.041 Sensitivity RNAalifold(seed): 0.284 Mastr(seed): 0.002 Positive Predictive Value RNAalifold(seed): 0.785 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.526 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.384 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.723 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	154 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.644 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.562 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.740 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.593 Mastr(seed): 0.040 Sensitivity Contrafold: 0.570 Mastr(seed): 0.002 Positive Predictive Value Contrafold: 0.618 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	100 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.540 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.396 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.738 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.572 Mastr(seed): 0.040 Sensitivity Sfold: 0.509 Mastr(seed): 0.002 Positive Predictive Value Sfold: 0.644 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.574 Mastr(seed): 0.040 Sensitivity ProbKnot: 0.556 Mastr(seed): 0.002 Positive Predictive Value ProbKnot: 0.593 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.575 Mastr(seed): 0.040 Sensitivity MaxExpect: 0.552 Mastr(seed): 0.002 Positive Predictive Value MaxExpect: 0.600 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.488 Mastr(seed): 0.041 Sensitivity McQFold: 0.468 Mastr(seed): 0.003 Positive Predictive Value McQFold: 0.510 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 Mastr(seed): 0.400 Sensitivity Murlet(seed): 0.319 Mastr(seed): 0.242 Positive Predictive Value Murlet(seed): 0.734 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.47043379369e-08	278 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.539 Mastr(seed): 0.040 Sensitivity Fold: 0.532 Mastr(seed): 0.002 Positive Predictive Value Fold: 0.548 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	276 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.527 Mastr(seed): 0.041 Sensitivity PknotsRG: 0.518 Mastr(seed): 0.003 Positive Predictive Value PknotsRG: 0.537 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.531 Mastr(seed): 0.040 Sensitivity UNAFold: 0.519 Mastr(seed): 0.002 Positive Predictive Value UNAFold: 0.544 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.633 Mastr(seed): 0.420 Sensitivity TurboFold(seed): 0.562 Mastr(seed): 0.270 Positive Predictive Value TurboFold(seed): 0.716 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	271 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.535 Mastr(seed): 0.042 Sensitivity RNAsubopt: 0.533 Mastr(seed): 0.003 Positive Predictive Value RNAsubopt: 0.538 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 271 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.525 Mastr(seed): 0.038 Sensitivity Afold: 0.514 Mastr(seed): 0.002 Positive Predictive Value Afold: 0.537 Mastr(seed): 0.639 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.476 Mastr(seed): 0.046 Sensitivity RNASLOpt: 0.438 Mastr(seed): 0.003 Positive Predictive Value RNASLOpt: 0.518 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.525 Mastr(seed): 0.040 Sensitivity RNAfold: 0.516 Mastr(seed): 0.002 Positive Predictive Value RNAfold: 0.535 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.603 Mastr(seed): 0.341 Sensitivity HotKnots: 0.588 Mastr(seed): 0.176 Positive Predictive Value HotKnots: 0.624 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.24270395587e-08	16 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.616 Mastr(seed): 0.365 Sensitivity RDfolder: 0.531 Mastr(seed): 0.202 Positive Predictive Value RDfolder: 0.721 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	152 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.505 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.334 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.766 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	253 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.482 Mastr(seed): 0.044 Sensitivity RNAshapes: 0.467 Mastr(seed): 0.003 Positive Predictive Value RNAshapes: 0.500 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.456 Mastr(seed): 0.041 Sensitivity CRWrnafold: 0.449 Mastr(seed): 0.003 Positive Predictive Value CRWrnafold: 0.465 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.353 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.140 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.891 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.377 Mastr(seed): 0.043 Sensitivity Vsfold5: 0.349 Mastr(seed): 0.003 Positive Predictive Value Vsfold5: 0.410 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	259 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.402 Mastr(seed): 0.043 Sensitivity Vsfold4: 0.363 Mastr(seed): 0.003 Positive Predictive Value Vsfold4: 0.447 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 259 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.370 Mastr(seed): 0.041 Sensitivity RNAwolf: 0.379 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.363 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.363 Mastr(seed): 0.132 Sensitivity CMfinder(seed): 0.184 Mastr(seed): 0.029 Positive Predictive Value CMfinder(seed): 0.716 Mastr(seed): 0.602 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	61 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.141 Mastr(seed): 0.097 Sensitivity Carnac(seed): 0.021 Mastr(seed): 0.014 Positive Predictive Value Carnac(seed): 0.962 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.292 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.173 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.494 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.486 Mastr(seed): 0.365 Sensitivity Alterna: 0.455 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.529 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	59 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.183 Mastr(seed): 0.040 Sensitivity NanoFolder: 0.209 Mastr(seed): 0.003 Positive Predictive Value NanoFolder: 0.163 Mastr(seed): 0.500 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	272 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.056 Mastr(seed): 0.041 Sensitivity RSpredict(seed): 0.017 Mastr(seed): 0.003 Positive Predictive Value RSpredict(seed): 0.187 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 272 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.057 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.004 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.884 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08		? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Mastr(seed): 0.540 Sensitivity Multilign(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value Multilign(seed): 0.625 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Mastr(seed): 0.540 Sensitivity PPfold(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value PPfold(seed): 0.833 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): 0.381 MCFold: 0.358 Sensitivity Mastr(seed): 0.220 MCFold: 0.409 Positive Predictive Value Mastr(seed): 0.670 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.02791190899e-08
Multilign(seed)	8 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.619 Multilign(seed): 0.575 Sensitivity PETfold_pre2.0(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.721 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.575 ContextFold: 0.566 Sensitivity Multilign(seed): 0.536 ContextFold: 0.514 Positive Predictive Value Multilign(seed): 0.625 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Multilign(seed): 0.575 Sensitivity CentroidAlifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Multilign(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.486 Multilign(seed): 0.536 Positive Predictive Value CentroidHomfold‑LAST: 0.708 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(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 Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	7 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.943 Multilign(seed): 0.572 Sensitivity Cylofold: 0.935 Multilign(seed): 0.532 Positive Predictive Value Cylofold: 0.951 Multilign(seed): 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.684 Multilign(seed): 0.575 Sensitivity IPknot: 0.586 Multilign(seed): 0.536 Positive Predictive Value IPknot: 0.804 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.886 Multilign(seed): 0.575 Sensitivity Pknots: 0.893 Multilign(seed): 0.536 Positive Predictive Value Pknots: 0.880 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 MXScarna(seed): 0.468 Sensitivity Multilign(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value Multilign(seed): 0.625 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.618 Multilign(seed): 0.575 Sensitivity CentroidFold: 0.514 Multilign(seed): 0.536 Positive Predictive Value CentroidFold: 0.750 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RNASampler(seed): 0.569 Sensitivity Multilign(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value Multilign(seed): 0.625 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Multilign(seed): 0.575 Sensitivity RNAalifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value RNAalifold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.596 Multilign(seed): 0.575 Sensitivity Contrafold: 0.521 Multilign(seed): 0.536 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.575 Sfold: 0.494 Sensitivity Multilign(seed): 0.536 Sfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.575 ProbKnot: 0.539 Sensitivity Multilign(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value Multilign(seed): 0.625 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.575 MaxExpect: 0.553 Sensitivity Multilign(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value Multilign(seed): 0.625 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.932 Multilign(seed): 0.575 Sensitivity McQFold: 0.936 Multilign(seed): 0.536 Positive Predictive Value McQFold: 0.929 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Murlet(seed): 0.518 Sensitivity Multilign(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value Multilign(seed): 0.625 Murlet(seed): 0.716 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): 0.575 Fold: 0.457 Sensitivity Multilign(seed): 0.536 Fold: 0.443 Positive Predictive Value Multilign(seed): 0.625 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.949 Multilign(seed): 0.575 Sensitivity PknotsRG: 0.943 Multilign(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 Multilign(seed): 0.625 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): 0.575 UNAFold: 0.483 Sensitivity Multilign(seed): 0.536 UNAFold: 0.457 Positive Predictive Value Multilign(seed): 0.625 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.644 Multilign(seed): 0.575 Sensitivity TurboFold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value TurboFold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.575 RNAsubopt: 0.478 Sensitivity Multilign(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.571 Afold: 0.480 Sensitivity Multilign(seed): 0.533 Afold: 0.443 Positive Predictive Value Multilign(seed): 0.619 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.588 Multilign(seed): 0.575 Sensitivity RNASLOpt: 0.514 Multilign(seed): 0.536 Positive Predictive Value RNASLOpt: 0.679 Multilign(seed): 0.625 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): 0.575 RNAfold: 0.472 Sensitivity Multilign(seed): 0.536 RNAfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAfold: 0.496 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): 0.575 HotKnots: 0.566 Sensitivity Multilign(seed): 0.536 HotKnots: 0.586 Positive Predictive Value Multilign(seed): 0.625 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: 0.593 Multilign(seed): 0.575 Sensitivity RDfolder: 0.486 Multilign(seed): 0.536 Positive Predictive Value RDfolder: 0.731 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.575 RNAshapes: 0.481 Sensitivity Multilign(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.575 CRWrnafold: 0.400 Sensitivity Multilign(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value Multilign(seed): 0.625 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold5: 0.423 Sensitivity Multilign(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value Multilign(seed): 0.625 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold4: 0.260 Sensitivity Multilign(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value Multilign(seed): 0.625 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.575 RNAwolf: 0.455 Sensitivity Multilign(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value Multilign(seed): 0.625 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.562 CMfinder(seed): 0.553 Sensitivity Multilign(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value Multilign(seed): 0.604 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.625 Multilign(seed): 0.575 Sensitivity Carnac(seed): 0.407 Multilign(seed): 0.536 Positive Predictive Value Carnac(seed): 0.966 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.575 Alterna: 0.414 Sensitivity Multilign(seed): 0.536 Alterna: 0.386 Positive Predictive Value Multilign(seed): 0.625 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.618 NanoFolder: 0.585 Sensitivity Multilign(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value Multilign(seed): 0.690 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RSpredict(seed): 0.437 Sensitivity Multilign(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value Multilign(seed): 0.625 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Mastr(seed): 0.540 Sensitivity Multilign(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value Multilign(seed): 0.625 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Multilign(seed): 0.575 Sensitivity PPfold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.575 MCFold: 0.340 Sensitivity Multilign(seed): 0.536 MCFold: 0.407 Positive Predictive Value Multilign(seed): 0.625 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
PPfold(seed)	8 PPfold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 PETfold_pre2.0(seed): 0.619 Sensitivity PPfold(seed): 0.536 PETfold_pre2.0(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 PETfold_pre2.0(seed): 0.721 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): 0.666 ContextFold: 0.566 Sensitivity PPfold(seed): 0.536 ContextFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 PPfold(seed): 0.666 Sensitivity CentroidAlifold(seed): 0.536 PPfold(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidHomfold‑LAST: 0.584 Sensitivity PPfold(seed): 0.536 CentroidHomfold‑LAST: 0.486 Positive Predictive Value PPfold(seed): 0.833 CentroidHomfold‑LAST: 0.708 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): N/A PPfold(seed): N/A Sensitivity TurboFold(20): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): N/A PPfold(seed): N/A Sensitivity PPfold(20): N/A PPfold(seed): N/A Positive Predictive Value PPfold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	7 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.943 PPfold(seed): 0.656 Sensitivity Cylofold: 0.935 PPfold(seed): 0.532 Positive Predictive Value Cylofold: 0.951 PPfold(seed): 0.815 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(seed): N/A CentroidAlifold(20): N/A Sensitivity PPfold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value PPfold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.684 PPfold(seed): 0.666 Sensitivity IPknot: 0.586 PPfold(seed): 0.536 Positive Predictive Value IPknot: 0.804 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.886 PPfold(seed): 0.666 Sensitivity Pknots: 0.893 PPfold(seed): 0.536 Positive Predictive Value Pknots: 0.880 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 MXScarna(seed): 0.468 Sensitivity PPfold(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value PPfold(seed): 0.833 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): N/A PPfold(seed): N/A Sensitivity RNAalifold(20): N/A PPfold(seed): N/A Positive Predictive Value RNAalifold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidFold: 0.618 Sensitivity PPfold(seed): 0.536 CentroidFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNASampler(seed): 0.569 Sensitivity PPfold(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value PPfold(seed): 0.833 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNAalifold(seed): 0.644 Sensitivity PPfold(seed): 0.536 RNAalifold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 RNAalifold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): N/A PPfold(seed): N/A Sensitivity RNASampler(20): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs MXScarna(20) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(20): N/A Sensitivity PPfold(seed): N/A MXScarna(20): N/A Positive Predictive Value PPfold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.666 Contrafold: 0.596 Sensitivity PPfold(seed): 0.536 Contrafold: 0.521 Positive Predictive Value PPfold(seed): 0.833 Contrafold: 0.689 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): N/A Murlet(20): N/A Sensitivity PPfold(seed): N/A Murlet(20): N/A Positive Predictive Value PPfold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.666 Sfold: 0.494 Sensitivity PPfold(seed): 0.536 Sfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.666 ProbKnot: 0.539 Sensitivity PPfold(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value PPfold(seed): 0.833 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.666 MaxExpect: 0.553 Sensitivity PPfold(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value PPfold(seed): 0.833 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.932 PPfold(seed): 0.666 Sensitivity McQFold: 0.936 PPfold(seed): 0.536 Positive Predictive Value McQFold: 0.929 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Murlet(seed): 0.518 Sensitivity PPfold(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value PPfold(seed): 0.833 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.666 Fold: 0.457 Sensitivity PPfold(seed): 0.536 Fold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 PPfold(seed): 0.666 Sensitivity PknotsRG: 0.943 PPfold(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.666 UNAFold: 0.483 Sensitivity PPfold(seed): 0.536 UNAFold: 0.457 Positive Predictive Value PPfold(seed): 0.833 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 TurboFold(seed): 0.644 Sensitivity PPfold(seed): 0.536 TurboFold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 TurboFold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.666 RNAsubopt: 0.478 Sensitivity PPfold(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.664 Afold: 0.480 Sensitivity PPfold(seed): 0.533 Afold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.666 RNASLOpt: 0.588 Sensitivity PPfold(seed): 0.536 RNASLOpt: 0.514 Positive Predictive Value PPfold(seed): 0.833 RNASLOpt: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.666 RNAfold: 0.472 Sensitivity PPfold(seed): 0.536 RNAfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs HotKnots Matthews Correlation Coefficient PPfold(seed): 0.666 HotKnots: 0.566 Sensitivity PPfold(seed): 0.536 HotKnots: 0.586 Positive Predictive Value PPfold(seed): 0.833 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RDfolder Matthews Correlation Coefficient PPfold(seed): 0.666 RDfolder: 0.593 Sensitivity PPfold(seed): 0.536 RDfolder: 0.486 Positive Predictive Value PPfold(seed): 0.833 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.666 RNAshapes: 0.481 Sensitivity PPfold(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.666 CRWrnafold: 0.400 Sensitivity PPfold(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value PPfold(seed): 0.833 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): N/A Carnac(20): N/A Sensitivity PPfold(seed): N/A Carnac(20): N/A Positive Predictive Value PPfold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold5: 0.423 Sensitivity PPfold(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value PPfold(seed): 0.833 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold4: 0.260 Sensitivity PPfold(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value PPfold(seed): 0.833 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.666 RNAwolf: 0.455 Sensitivity PPfold(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value PPfold(seed): 0.833 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.662 CMfinder(seed): 0.553 Sensitivity PPfold(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value PPfold(seed): 0.833 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Carnac(seed): 0.625 Sensitivity PPfold(seed): 0.536 Carnac(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): N/A PPfold(seed): N/A Sensitivity RSpredict(20): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): 0.666 Alterna: 0.414 Sensitivity PPfold(seed): 0.536 Alterna: 0.386 Positive Predictive Value PPfold(seed): 0.833 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.698 NanoFolder: 0.585 Sensitivity PPfold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value PPfold(seed): 0.879 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RSpredict(seed): 0.437 Sensitivity PPfold(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): N/A PPfold(seed): N/A Sensitivity Mastr(20): N/A PPfold(seed): N/A Positive Predictive Value Mastr(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Mastr(seed): 0.540 Sensitivity PPfold(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value PPfold(seed): 0.833 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Multilign(seed): 0.575 Sensitivity PPfold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): 0.666 MCFold: 0.340 Sensitivity PPfold(seed): 0.536 MCFold: 0.407 Positive Predictive Value PPfold(seed): 0.833 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
MCFold	17 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 MCFold: 0.336 Sensitivity PETfold_pre2.0(seed): 0.663 MCFold: 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.829 MCFold: 0.303 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.36130997681e-08	48 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.449 MCFold: 0.290 Sensitivity ContextFold: 0.402 MCFold: 0.320 Positive Predictive Value ContextFold: 0.511 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 MCFold: 0.358 Sensitivity CentroidAlifold(seed): 0.642 MCFold: 0.409 Positive Predictive Value CentroidAlifold(seed): 0.944 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	48 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.487 MCFold: 0.290 Sensitivity CentroidHomfold‑LAST: 0.422 MCFold: 0.320 Positive Predictive Value CentroidHomfold‑LAST: 0.570 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.857 MCFold: 0.291 Sensitivity TurboFold(20): 0.744 MCFold: 0.323 Positive Predictive Value TurboFold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MCFold: 0.291 Sensitivity PETfold_pre2.0(20): 0.759 MCFold: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.962 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.840 MCFold: 0.291 Sensitivity PPfold(20): 0.737 MCFold: 0.323 Positive Predictive Value PPfold(20): 0.961 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	44 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.771 MCFold: 0.294 Sensitivity Cylofold: 0.749 MCFold: 0.323 Positive Predictive Value Cylofold: 0.799 MCFold: 0.284 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MCFold: 0.291 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.323 Positive Predictive Value CentroidAlifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.503 MCFold: 0.290 Sensitivity IPknot: 0.457 MCFold: 0.320 Positive Predictive Value IPknot: 0.562 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.707 MCFold: 0.296 Sensitivity Pknots: 0.676 MCFold: 0.325 Positive Predictive Value Pknots: 0.747 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.538 MCFold: 0.358 Sensitivity MXScarna(seed): 0.502 MCFold: 0.409 Positive Predictive Value MXScarna(seed): 0.586 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.70887622364e-08	5 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.844 MCFold: 0.291 Sensitivity RNAalifold(20): 0.722 MCFold: 0.323 Positive Predictive Value RNAalifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.486 MCFold: 0.290 Sensitivity CentroidFold: 0.436 MCFold: 0.320 Positive Predictive Value CentroidFold: 0.550 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.621 MCFold: 0.354 Sensitivity RNASampler(seed): 0.546 MCFold: 0.415 Positive Predictive Value RNASampler(seed): 0.713 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08	5 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.862 MCFold: 0.291 Sensitivity Multilign(20): 0.752 MCFold: 0.323 Positive Predictive Value Multilign(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	15 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.664 MCFold: 0.358 Sensitivity RNAalifold(seed): 0.537 MCFold: 0.409 Positive Predictive Value RNAalifold(seed): 0.828 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	5 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.840 MCFold: 0.291 Sensitivity RNASampler(20): 0.714 MCFold: 0.323 Positive Predictive Value RNASampler(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.837 MCFold: 0.291 Sensitivity MXScarna(20): 0.752 MCFold: 0.323 Positive Predictive Value MXScarna(20): 0.935 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.471 MCFold: 0.290 Sensitivity Contrafold: 0.440 MCFold: 0.320 Positive Predictive Value Contrafold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.741 MCFold: 0.291 Sensitivity Murlet(20): 0.594 MCFold: 0.323 Positive Predictive Value Murlet(20): 0.929 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.441 MCFold: 0.290 Sensitivity Sfold: 0.399 MCFold: 0.320 Positive Predictive Value Sfold: 0.497 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.479 MCFold: 0.290 Sensitivity ProbKnot: 0.456 MCFold: 0.320 Positive Predictive Value ProbKnot: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.457 MCFold: 0.290 Sensitivity MaxExpect: 0.424 MCFold: 0.320 Positive Predictive Value MaxExpect: 0.502 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.652 MCFold: 0.290 Sensitivity McQFold: 0.631 MCFold: 0.320 Positive Predictive Value McQFold: 0.681 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.456 MCFold: 0.354 Sensitivity Murlet(seed): 0.307 MCFold: 0.415 Positive Predictive Value Murlet(seed): 0.685 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	48 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.472 MCFold: 0.290 Sensitivity Fold: 0.443 MCFold: 0.320 Positive Predictive Value Fold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.537 MCFold: 0.290 Sensitivity PknotsRG: 0.522 MCFold: 0.320 Positive Predictive Value PknotsRG: 0.560 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.423 MCFold: 0.290 Sensitivity UNAFold: 0.394 MCFold: 0.320 Positive Predictive Value UNAFold: 0.463 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.600 MCFold: 0.343 Sensitivity TurboFold(seed): 0.518 MCFold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 MCFold: 0.302 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	48 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.416 MCFold: 0.290 Sensitivity RNAsubopt: 0.393 MCFold: 0.320 Positive Predictive Value RNAsubopt: 0.451 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.280 MCFold: 0.263 Sensitivity Afold: 0.274 MCFold: 0.294 Positive Predictive Value Afold: 0.299 MCFold: 0.247 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 0.000706081118372	48 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.489 MCFold: 0.290 Sensitivity RNASLOpt: 0.442 MCFold: 0.320 Positive Predictive Value RNASLOpt: 0.549 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.417 MCFold: 0.290 Sensitivity RNAfold: 0.391 MCFold: 0.320 Positive Predictive Value RNAfold: 0.455 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.480 MCFold: 0.290 Sensitivity HotKnots: 0.464 MCFold: 0.320 Positive Predictive Value HotKnots: 0.506 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.505 MCFold: 0.296 Sensitivity RDfolder: 0.428 MCFold: 0.325 Positive Predictive Value RDfolder: 0.605 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.779 MCFold: 0.291 Sensitivity CMfinder(20): 0.617 MCFold: 0.323 Positive Predictive Value CMfinder(20): 0.988 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.438 MCFold: 0.290 Sensitivity RNAshapes: 0.408 MCFold: 0.320 Positive Predictive Value RNAshapes: 0.481 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.411 MCFold: 0.290 Sensitivity CRWrnafold: 0.380 MCFold: 0.320 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.821 MCFold: 0.291 Sensitivity Carnac(20): 0.684 MCFold: 0.323 Positive Predictive Value Carnac(20): 0.989 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	48 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.555 MCFold: 0.290 Sensitivity Vsfold5: 0.517 MCFold: 0.320 Positive Predictive Value Vsfold5: 0.604 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.435 MCFold: 0.290 Sensitivity Vsfold4: 0.387 MCFold: 0.320 Positive Predictive Value Vsfold4: 0.498 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.376 MCFold: 0.290 Sensitivity RNAwolf: 0.364 MCFold: 0.320 Positive Predictive Value RNAwolf: 0.400 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.499 MCFold: 0.352 Sensitivity CMfinder(seed): 0.385 MCFold: 0.408 Positive Predictive Value CMfinder(seed): 0.657 MCFold: 0.315 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): 0.566 MCFold: 0.354 Sensitivity Carnac(seed): 0.332 MCFold: 0.415 Positive Predictive Value Carnac(seed): 0.971 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.70361883708e-09	5 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.672 MCFold: 0.291 Sensitivity RSpredict(20): 0.549 MCFold: 0.323 Positive Predictive Value RSpredict(20): 0.830 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	45 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.399 MCFold: 0.296 Sensitivity Alterna: 0.369 MCFold: 0.325 Positive Predictive Value Alterna: 0.444 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.304 MCFold: 0.248 Sensitivity NanoFolder: 0.343 MCFold: 0.283 Positive Predictive Value NanoFolder: 0.281 MCFold: 0.229 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): 0.522 MCFold: 0.358 Sensitivity RSpredict(seed): 0.441 MCFold: 0.409 Positive Predictive Value RSpredict(seed): 0.627 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.12262428713e-08	5 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.561 MCFold: 0.291 Sensitivity Mastr(20): 0.459 MCFold: 0.323 Positive Predictive Value Mastr(20): 0.693 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	15 Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): 0.381 MCFold: 0.358 Sensitivity Mastr(seed): 0.220 MCFold: 0.409 Positive Predictive Value Mastr(seed): 0.670 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.02791190899e-08	8 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.575 MCFold: 0.340 Sensitivity Multilign(seed): 0.536 MCFold: 0.407 Positive Predictive Value Multilign(seed): 0.625 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): 0.666 MCFold: 0.340 Sensitivity PPfold(seed): 0.536 MCFold: 0.407 Positive Predictive Value PPfold(seed): 0.833 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0

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