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Table 1 Total SP scores on the full-length BAliBASE 3.0 subsets.

From: MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

MSA tools RV11 RV12 RV20 RV30 RV40 RV50
MSACompro 73.14 94.84 93.30 87.16 92.11 91.41
Clustalw 50.06 86.44 85.16 69.76 78.93 74.24
DIALIGN-TX 51.52 89.18 87.87 73.64 83.64 82.28
FSA 50.28 92.38 86.7 66.27 85.87 78.21
MAFFT 55.13 88.82 89.33 79.08 87.55 84.69
MSAProbs 68.18 94.65 92.81 83.19 92.47 90.76
MUSCLE 57.16 91.54 88.91 78.24 86.49 83.52
Opal 66.18 93.70 90.39 80.18 76.25 87.36
POA 37.96 83.19 85.28 69.18 78.22 71.49
Probalign 69.51 94.64 92.57 82.03 92.19 88.86
ProbCons 66.97 94.12 91.67 81.28 90.34 89.41
T-coffee 66.77 94.08 91.61 80.57 89.96 89.43
  1. Bold denotes the highest scores. MSACompro yielded the highest SP scores on all the subsets except RV40. On some datasets such as RV11 and RV30, the improvement is substantial.