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Table 1 Change in average Q-score according to the number of sequences being aligned

From: DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

  Total sequences Clustal Omega DECIPHER MAFFT MUSCLE PASTAa
HOMSTRAD-modb Maximum score 0.898 0.910 0.920 0.881 0.921
Change from max 2 −0.013 −0.02 −0.045 0.000 N/A
125 0.000 0.000 0.000 −0.007 0.000
250 −0.009 −0.011 −0.028 −0.028 −0.003
500 −0.013 −0.014 −0.037 −0.028 −0.016
1000 −0.035 −0.011 −0.049 −0.048 −0.026
2000 −0.035 −0.019 −0.054 −0.088 −0.028
4000 −0.069 −0.030 −0.077 −0.128 −0.049
PREFAB-modb Maximum score 0.875 0.908 0.923 0.855 0.900
Change from max 2 −0.067 −0.085 −0.123 −0.047 N/A
125 0.000 0.000 0.000 0.000 0.000
250 −0.022 −0.007 −0.057 −0.011 −0.015
500 −0.022 −0.004 −0.068 −0.026 −0.029
1000 −0.034 −0.023 −0.090 −0.056 −0.045
2000 −0.069 −0.037 −0.107 −0.093 −0.080
4000 −0.121 −0.026 −0.098 −0.156 −0.116
  1. aScores for aligning two sequences are listed as “N/A” because PASTA cannot perform pairwise alignment
  2. bResults for the subset of reference alignments with at least 4,000 reference sequences are shown (297 alignments for HOMSTRAD-mod and 201 alignments for PREFAB-mod)
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