Table 4.

Performance of MCALIGN2 and AVID compared by proportions of correctly aligned sites based on a GTR model

Simulated		Proportion of matched bases
t	Θ	AVID	MCALIGN2(JC)	MCALIGN2(K2P)	MCALIGN2(GTR)
0.05	0.225	0.991 (0.0085)	0.993 (0.0057)	0.993 (0.0057)	0.993 (0.0057)
0.10	0.225	0.973 (0.0141)	0.978 (0.0127)	0.979 (0.0127)	0.979 (0.0127)
0.15	0.225	0.946 (0.0283)	0.954 (0.0212)	0.956 (0.0184)	0.958 (0.0184)
0.20	0.225	0.904 (0.0325)	0.916 (0.0283)	0.920 (0.0269)	0.922 (0.0269)
0.25	0.225	0.852 (0.0452)	0.867 (0.0438)	0.873 (0.0410)	0.876 (0.0396)
0.30	0.225	0.795 (0.0566)	0.811 (0.0495)	0.824 (0.0481)	0.831 (0.0481)
0.15	0.10	0.980 (0.0141)	0.982 (0.0113)	0.982 (0.0113)	0.983 (0.0113)
0.15	0.30	0.913 (0.0283)	0.935 (0.0226)	0.936 (0.0212)	0.941 (0.0212)
0.15	0.40	0.876 (0.0354)	0.900 (0.0311)	0.905 (0.0297)	0.916 (0.0283)

Proportion of matched bases from 200 replicates for each combination of t and θ, with sequences of length 500 base pairs. Standard deviation of mean is shown after the proportion of matched bases in parentheses. Here MCALIGN2 is tested by assuming either the correct model of DNA evolution(GTR) or the incorrect models (JC and K2P).