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Table 2 Performance of seven protein multi-alignment programs on IRMBASE using column scores as quality criterion. Thus, percentage values denote the percentage of correct alignment columns of the ROSE motifs in IRMBASE

From: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

Method ref1 ref2 ref3 Total
DIALIGN-T 82.28% 78.36% 79.71% 80.12%
DIALIGN 2.2 79.46% 77.82% 78.24% 78.51%
T-COFFEE 1.37 75.35% 66.60% 69.21% 70.19%
PROBCONS 1.09 33.13% 37.95% 51.26% 40.78%
POA V2 73.00% 12.46% 07.45% 30.97%
MUSCLE 3.5 09.41% 10.89% 22.37% 14.22%
CLUSTAL W 1.83 00.00% 00.83% 05.14% 01.92%