Table 2.

Performance of MCALIGN2(DP), MCALIGN(MC) and PairHMM_KM compared by the estimator of divergenct time corrected by the Jukes-Cantor model

Simulated			Alignment Estimated
t	Θ	Alignment Known	PairHMM_KM	MC	DP
0.05	0.225	0.0502 (0.0107)	0.0496 (0.0103)	0.0499 (0.0104)	0.0501 (0.0103)
0.10	0.225	0.0998 (0.0146)	0.0987 (0.0152)	0.0994 (0.0153)	0.0989 (0.0154)
0.15	0.225	0.1493 (0.0208)	0.1482 (0.0226)	0.1507 (0.0230)	0.1487 (0.0208)
0.20	0.225	0.2025 (0.0241)	0.1994 (0.0267)	0.2053 (0.0263)	0.2001 (0.0256)
0.25	0.225	0.2515 (0.0286)	0.2440 (0.0348)	0.2593 (0.0346)	0.2476 (0.0319)
0.30	0.225	0.3003 (0.0311)	0.2955 (0.0419)	0.3162 (0.0525)	0.2981 (0.0349)
0.15	0.10	0.1519 (0.0198)	0.1503 (0.0189)	0.1502 (0.0189)	0.1500 (0.0188)
0.15	0.30	0.1515 (0.0202)	0.1507 (0.0226)	0.1566 (0.0234)	0.1523 (0.0218)
0.15	0.40	0.1512 (0.0194)	0.1480 (0.0220)	0.1645 (0.0263)	0.1516 (0.0213)

Estimates of sequence divergence, t, and proportion of matched bases 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.