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Table 3 Significance of differences in BAliBASE 3.0 SP/TC scores

From: MSARC: Multiple sequence alignment by residue clustering

Aligner   RV11 RV12 RV20 RV30 RV40 RV50 Total
Non-progressive methods      
DIALIGN-T   + 8.6 e 8 + 1.5 e 6 + 7.7 e 9 + 2.2 e 8 + 1.3 e 7 + 9.6 e 5 + 2.7 e 6 + 0.0024 + 2.1 e 9 + 4.9 e 8 + 0.00098 + 0.027 + 5.3 e 36 + 3.6 e 26
FSA   + 8.6 e 8 + 1.2 e 6 + 3.5 e 6 + 0.00012 + 3.6 e 8 + 1.2 e 6 + 2.6 e 6 + 8.5 e 6 + 8.3 e 9 + 1.2 e 6 + 0.00081 + 0.021 + 3.6 e 34 + 3.5 e 27
PicXAA   + 0.048 + ( 0.53 ) ( 0.82 ) ( 0.98 ) ( 0.055 ) 0.018 2.8 e 5 7.2 e 6 + ( 0.11 ) ( 0.052 ) ( 0.063 ) ( 0.37 ) 0.0079 1.3 e 6
Progressive methods      
Clustal Ω   + 2.6 e 7 + 5.1 e 5 + 2.4 e 5 + 0.00019 + 0.0048 0.00054 0.020 0.00060 + 2.2 e 6 + ( 0.16 ) + 0.017 ( 0.77 ) + 1.1 e 13 + ( 0.30 )
DIALIGN-TX   + 1.0 e 7 + 1.3 e 6 + 6.2 e 8 + 4.0 e 7 + 2.3 e 7 + 0.00040 + 8.7 e 6 + 0.038 + 2.8 e 9 + 1.3 e 7 + 0.0017 + ( 0.066 ) + 3.1 e 34 + 9.5 e 23
MAFFT   + 0.0031 + ( 0.11 ) + 0.00085 + 0.005 ( 0.64 ) ( 0.052 ) 0.0009 0.0007 + 0.0005 + ( 0.07 ) ( 0.072 ) ( 0.062 ) + 0.028 ( 0.55 )
MSAProbs   + 0.028 + ( 0.23 ) ( 0.90 ) ( 0.67 ) 0.011 0.00032 0.00017 1.4 e 5 + ( 0.61 ) + 0.048 0.010 0.0086 0.020 5.9 e 8
MUSCLE   + 7.3 e 6 + 0.00017 + 2.8 e 6 + 0.00015 + 0.00015 + ( 0.15 ) + ( 0.19 ) + ( 0.52 ) + 7.6 e 9 + 2.8 e 6 + 0.010 + ( 0.072 ) + 2.9 e 22 + 3.3 e 12
Probalign   + ( 0.67 ) + ( 0.52 ) ( 0.63 ) ( 0.88 ) 0.032 6.8 e 5 0.0099 0.00056 + ( 0.62 ) + ( 0.060 ) ( 0.18 ) ( 0.32 ) 0.019 6.0 e 6
ProbCons   + 0.021 + 0.037 + 0.0042 + ( 0.19 ) + 0.028 ( 0.19 ) ( 0.15 ) 0.010 + 0.00026 + 0.022 ( 0.12 ) ( 0.17 ) + 0.00087 + ( 0.93 )
T-Coffee   + 0.0024 + 0.016 + 0.0017 + 0.013 + 0.0075 ( 0.51 ) ( 0.29 ) ( 0.099 ) + 9.7 e 5 + ( 0.29 ) 0.048 0.026 + 1.3 e 5 + ( 0.70 )
  1. Entries show p-values indicating the significance of the mean difference of SP/TC scores between MSARC and other aligners as measured using the Wilcoxon matched-pair signed-rank test. A + means that MSARC had a higher mean score while a − means MSARC had a lower mean score. Nonsignificant p-values (>0.05) are shown in parentheses.