Table 2.

Performance of MCALIGN and Other Alignment Methods Compared by Simulation

Simulated		Alignment known	Alignment estimated						MCALIGN efficiency
t	θ		DIALIGN	LAGAN	AVID	CLUSTAL	HANDEL	MCALIGN
0.05	0.225	0.0488 (0.0159)	0.0529 (0.0192)	0.0549 (0.0194)	0.0499 (0.0161)	0.0525 (0.0185)	0.0485 (0.0165)	0.0487 (0.0162)	0.97
0.10	0.225	0.0995 (0.0232)	0.1121 (0.0327)	0.1125 (0.0330)	0.1024 (0.0255)	0.1115 (0.0364)	0.1000 (0.0328)	0.0988 (0.0241)	0.93
0.15	0.225	0.1519 (0.0311)	0.1818 (0.0561)	0.1749 (0.0511)	0.1585 (0.0352)	0.1807 (0.0656)	0.1562 (0.0480)	0.1510 (0.0324)	0.92
0.20	0.225	0.2043 (0.0366)	0.2491 (0.0769)	0.2443 (0.0719)	0.2132 (0.0435)	0.2518 (0.0946)	0.2107 (0.0652)	0.2022 (0.0388)	0.89
0.25	0.225	0.2502 (0.0426)	0.3216 (0.1055)	0.3039 (0.0824)	0.2629 (0.0467)	0.3122 (0.1011)	0.2537 (0.0631)	0.2519 (0.0438)	0.94
0.30	0.225	0.2968 (0.0470)	0.3876 (0.1181)	0.3670 (0.1029)	0.3103 (0.0469)	0.3799 (0.1281)	0.2923 (0.0703)	0.2974 (0.0531)	0.75
0.15	0.1	0.1531 (0.0317)	0.1612 (0.0359)	0.1628 (0.0391)	0.1539 (0.0321)	0.1592 (0.0366)	0.1538 (0.0383)	0.1524 (0.0315)	1.01
0.15	0.3	0.1504 (0.0276)	0.1958 (0.0656)	0.1904 (0.0625)	0.1652 (0.0351)	0.1909 (0.0666)	0.1573 (0.0382)	0.1504 (0.0276)	1.00
0.15	0.4	0.1498 (0.0303)	0.2140 (0.0899)	0.2085 (0.0812)	0.1731 (0.0469)	0.2185 (0.1030)	0.1621 (0.0489)	0.1480 (0.0325)	0.87

Estimates of sequence divergence, t, from 200 replicates per t value, with sequences of length 200 base pairs. Estimated root mean square error (e.r.m.s.e.) is shown in parentheses.