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Table 7 Performance of aligners on the BAliBASE benchmark database

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

  SP
Aligner RV11 (38) RV12 (44) RV20 (41) RV30 (30) RV40(49) RV50 (16) Overall (218)
MMSA 0.642 0.929 0.918 0.839 0.911 0.895 0.856
ProbCons 0.670 0.941 0.917 0.845 0.903 0.894 0.862
T-Coffee 0.656 0.939 0.914 0.837 0.893 0.895 0.856
MUSCLE 0.572 0.915 0.889 0.814 0.865 0.835 0.815
MAFFT 0.662 0.935 0.927 0.868 0.926 0.903 0.870
ClustalW 0.501 0.865 0.852 0.725 0.789 0.742 0.746
ClustalO 0.590 0.906 0.902 0.862 0.902 0.862 0.837
Kalign 0.605 0.912 0.900 0.813 0.884 0.820 0.822
MSAProbs 0.682 0.946 0.928 0.865 0.925 0.908 0.876
  Time(sec)
Aligner RV11 (38) RV12 (44) RV20 (41) RV30 (30) RV40(49) RV50 (16) Overall (218)
MMSA 0.817 1.772 69.797 119.424 38.725 38.453 44.831
ProbCons 2.481 7.052 142.641 297.473 108.307 124.235 113.698
T-Coffee 15.058 23.310 259.227 646.212 202.948 210.856 226.269
MUSCLE 0.701 0.824 5.490 7.538 9.519 7.002 5.179
MAFFT 0.840 1.580 14.071 25.811 27.455 18.434 14.698
ClustalW 0.310 0.923 13.281 25.231 8.155 8.982 9.480
ClustalO 0.406 0.747 4.224 4.824 5.214 4.790 3.368
Kalign 0.054 0.090 0.435 0.562 0.559 0.411 0.352
MSAProbs 2.092 6.436 141.371 295.506 86.463 102.198 105.678
  1. The values in the upper table show the average sum-of-pairs (SP) score and the values in the lower table mean run time achieved by different aligners for each of the six BAliBASE references. The number of alignments in each reference is given in parentheses. Overall values for the entire database are reported in the last column. The best results in each column are shown in bold