Table 1.

SP scores for ClustalW, T-Coffee, MSAM and MSAM-H on substitution rates of 0.1

	l = 200		l = 400		l = 800		l = 1000
indel	0.001	0.005	0.001	0.005	0.001	0.005	0.001	0.005
Clustal	0.785	0.408	0.790	0.439	0.801	0.437	0.779	0.356
T-Coffee	0.534	0.419	0.602	0.429	0.615	0.431	0.577	0.333
POY	0.838	0.442	0.817	0.405	0.805	0.430	0.784	0.320
MSAM-H	0.652	0.334	0.467	0.291	0.489	0.215	0.476	0.187
MSAM	0.754	0.366	0.560	0.328	0.586	0.236	0.572	0.217