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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.