Table 1. BAliBASE scores and times.

Method	Q	TC	CPU
MUSCLE	0.896	0.747	97
MUSCLE-p	0.883	0.727	52
T-Coffee	0.882	0.731	1500
NWNSI	0.881	0.722	170
CLUSTALW	0.860	0.690	170
FFTNS1	0.844	0.646	16

Average Q and TC scores for each method on BAliBASE are shown, together with the total CPU time in seconds. Align-m aborted on two alignments; average scores on the remainder were Q = 0.852 and TC = 0.670, requiring 2202 s.