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 | ||||||
[i] 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.