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Table 8 Performance of aligners on the SABmark benchmark database

From: Comprehensive comparison of graph based multiple protein sequence alignment strategies

 

Twilight zone (209)

Superfamily (425)

Aligner

FD

FM

Time(sec)

FD

FM

Time(sec)

MMSA

26.74

19.13

1.97

55.40

42.10

1.60

MMSA::treeBF

27.39

19.45

7.35

55.51

42.07

5.75

ProbCons

28.23

20.65

1.36

56.26

43.26

1.37

T-Coffee

27.75

20.50

2.34

55.86

43.03

2.21

MUSCLE

23.32

16.28

0.34

52.43

39.60

0.36

MAFFT

25.70

18.84

0.70

55.01

42.22

0.55

ClustalW

21.85

14.80

0.21

50.29

37.76

0.21

ClustalO

22.17

16.49

0.22

52.63

40.85

0.17

Kalign

21.87

15.24

0.06

49.70

38.02

0.05

MSAProbs

28.57

20.86

1.11

57.13

43.92

1.16

  1. Columns show the average developer (FD) score, modeller (FM) score and run time achieved by different aligners for the "Twilight Zone" and "Superfamily" sets in the SABmark database. The number of alignments in each reference is given in parentheses. The best results in each column are shown in bold
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BMC Bioinformatics

ISSN: 1471-2105

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