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) |