Table 3.

Accuracy scores. The average accuracy, measured by the Q score, is reported for each method on each set of reference alignments.

Method	PREFAB	BAliBASE	SABmark	SMART
MUSCLE	0.648	0.896	0.430	0.856
MUSCLE-prog	0.634	0.883	0.427	0.837
FFTNS1	0.619	0.844	0.376	0.815
MUSCLE-fast	0.616	0.849	0.396	0.813
CLUSTALW	0.588	0.860	0.404	0.823
POA-blast	0.577	0.839	0.352	0.788
POA	0.576	0.834	0.280	0.797