Table 1.

Results from the BAliBASE motif reference set, subset RV913 containing sequences with 40–80% sequence identity

Method	Mean general alignment score	Mean motif score
T-Coffee	0.94	0.95
Clustal Omega	0.93	0.86
Clustal Omega refined with KMAD	0.93	0.90
KMAD	0.91	0.92
MAFFT	0.92	0.93
MUSCLE	0.92	0.93
ClustalW2	0.93	0.93

More BAliBASE results and also PREFAB benchmarking results are available at the KMAD website.