Table 3.

Performance of MCALIGN2(DP), MCALIGN(MC) and PairHMM_KM compared by examining the proportions of correctly aligned sites.

Simulated		Proportions of correctly aligned sites.
t	Θ	PAIRHMM	MC	DP
0.05	0.225	0.992 (0.0072)	0.992 (0.0078)	0.993 (0.0074)
0.10	0.225	0.977 (0.0133)	0.977 (0.0137)	0.977 (0.0127)
0.15	0.225	0.954 (0.0210)	0.951 (0.0235)	0.955 (0.0186)
0.20	0.225	0.920 (0.0300)	0.915 (0.0345)	0.922 (0.0293)
0.25	0.225	0.868 (0.0416)	0.850 (0.0596)	0.869 (0.0433)
0.30	0.225	0.810 (0.0500)	0.761 (0.0853)	0.813 (0.0511)
0.15	0.10	0.984 (0.0116)	0.983 (0.0102)	0.983 (0.0108)
0.15	0.30	0.933 (0.0224)	0.925 (0.0292)	0.933 (0.0246)
0.15	0.40	0.905 (0.0325)	0.894 (0.0376)	0.906 (0.0329)

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.