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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