Table 5.

Performance of MCALIGN2 and AVID compared by estimator of divergence time based on a General Time-Reversible Model

Simulated			Alignment Estimated
t	Θ	Alignment Known	AVID	MCALIGN2(JC)	MCALIGN2(K2P)	MCALIGN2(GTR)
0.05	0.225	0.0504 (0.0100)	0.0523 (0.0181)	0.0501 (0.0100)	0.0500 (0.0100)	0.0500 (0.0100)
0.10	0.225	0.0991 (0.0145)	0.1023 (0.0159)	0.0981 (0.0151)	0.0976 (0.0149)	0.0983 (0.0149)
0.15	0.225	0.1522 (0.0191)	0.1575 (0.0226)	0.1496 (0.0192)	0.1494 (0.0192)	0.1502 (0.0194)
0.20	0.225	0.2034 (0.0225)	0.2131 (0.0283)	0.1985 (0.0238)	0.1978 (0.0239)	0.2003 (0.0235)
0.25	0.225	0.2531 (0.0286)	0.2699 (0.0383)	0.2493 (0.0316)	0.2453 (0.0308)	0.2491 (0.0311)
0.30	0.225	0.3003 (0.0302)	0.3222 (0.0420)	0.2944 (0.0324)	0.2914 (0.0311)	0.2987 (0.0323)
0.15	0.10	0.1520 (0.0207)	0.1528 (0.0219)	0.1510 (0.0203)	0.1508 (0.0203)	0.1510 (0.0204)
0.15	0.30	0.1509 (0.0200)	0.1634 (0.0301)	0.1489 (0.0207)	0.1470 (0.0208)	0.1499 (0.0207)
0.15	0.40	0.1526 (0.0208)	0.1794 (0.0398)	0.1507 (0.0213)	0.1477 (0.0203)	0.1508 (0.0211)

Estimates of sequence divergence,t, from 200 replicates for each combination of t and θ, with sequences of Length 500 base pairs. Estimated root mean square error (e.r.m.s.e.) is shown after divergence time in parentheses. Here MCALIGN2 is tested by assuming either the correct model of DNA evolution(GTR) or the incorrect models (JC and K2P).