Table 3.
Proportions of Correctly Matched Bases From MCALIGN and Other Alignment Methods Compared by Simulation
|
Simulated |
Proportion of matched bases |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| t |
θ |
DIALIGN |
LAGAN |
AVID |
CLUSTAL |
HANDEL |
MCALIGN |
||||||
| 0.05 | 0.225 | 0.986 (0.0014) | 0.987 (0.0014) | 0.990 (0.0011) | 0.983 (0.0022) | 0.969 (0.0015) | 0.991 (0.00085) | ||||||
| 0.10 | 0.225 | 0.963 (0.0023) | 0.966 (0.0023) | 0.977 (0.0016) | 0.960 (0.0035) | 0.944 (0.0022) | 0.980 (0.0015) | ||||||
| 0.15 | 0.225 | 0.925 (0.0036) | 0.932 (0.0037) | 0.949 (0.0029) | 0.913 (0.0058) | 0.874 (0.0033) | 0.954 (0.0026) | ||||||
| 0.20 | 0.225 | 0.892 (0.0044) | 0.901 (0.0046) | 0.928 (0.0035) | 0.871 (0.0078) | 0.820 (0.0043) | 0.935 (0.0033) | ||||||
| 0.25 | 0.225 | 0.839 (0.0050) | 0.848 (0.0053) | 0.887 (0.0042) | 0.812 (0.0079) | 0.776 (0.0039) | 0.894 (0.0046) | ||||||
| 0.30 | 0.225 | 0.776 (0.0058) | 0.792 (0.0066) | 0.838 (0.0055) | 0.751 (0.0096) | 0.702 (0.0047) | 0.844 (0.0057) | ||||||
| 0.15 | 0.1 | 0.973 (0.0019) | 0.978 (0.0020) | 0.984 (0.0015) | 0.973 (0.0029) | 0.948 (0.0034) | 0.986 (0.0012) | ||||||
| 0.15 | 0.3 | 0.903 (0.0041) | 0.909 (0.0043) | 0.933 (0.0032) | 0.894 (0.0062) | 0.854 (0.0036) | 0.944 (0.0027) | ||||||
| 0.15
|
0.4
|
0.863 (0.0041)
|
0.902 (0.0037)
|
0.902 (0.0037)
|
0.822 (0.0085)
|
0.800 (0.0035)
|
0.916 (0.0031)
|
||||||
-
Data are from 200 replicates per parameter value combination, with sequences of length 200 base pairs. Standard error of the mean is shown in parentheses.
