Table 1.
The first column lists the individual methods used
| Alignment method | Default %CS | VarCov weight | THG weight | ALT weight | ACC weight | No weight |
|---|---|---|---|---|---|---|
| CLUSTALW v1.83* | 61.15 | 1.77 | 1.41 | 1.86 | 1.01 | 1.00 |
| DIALIGN | 55.71 | 1.31 | 1.33 | 1.83 | 0.92 | 1.00 |
| DIALIGN-T* | 57.92 | 1.34 | 1.33 | 1.83 | 0.95 | 1.00 |
| FFTNS1 | 58.27 | 0.81 | 0.74 | 0.64 | 0.96 | 1.00 |
| FFTNS2 | 60.47 | 0.40 | 0.64 | 0.44 | 1.00 | 1.00 |
| FFTNSI | 63.07 | 0.17 | 0.64 | 0.44 | 1.04 | 1.00 |
| FINSI* | 64.22 | 0.79 | 0.74 | 0.38 | 1.06 | 1.00 |
| GINSI | 63.43 | 0.50 | 0.74 | 0.38 | 1.04 | 1.00 |
| Muscle v3.52 | 64.49 | 1.02 | 0.85 | 0.54 | 1.06 | 1.00 |
| Muscle v6.0* | 66.04 | 0.78 | 0.56 | 0.24 | 1.09 | 1.00 |
| PCMA* | 63.73 | 1.41 | 0.94 | 0.75 | 1.05 | 1.00 |
| POA-global* | 51.90 | 1.37 | 1.87 | 2.51 | 0.85 | 1.00 |
| POA-local | 49.28 | 1.42 | 1.87 | 2.51 | 0.81 | 1.00 |
| ProbCons v1.09* | 66.41 | 0.73 | 0.56 | 0.24 | 1.09 | 1.00 |
| T-Coffee v2.03* | 65.37 | 1.18 | 0.78 | 0.42 | 1.08 | 1.00 |
| %CS for M-Coffee15 | 67.33 | 66.96 | 65.79 | 67.16 | 67.11 | |
| %CS for M-Coffee8 | 67.32 | 66.33 | 64.89 | 67.85 | 67.75 |
Methods in boldface marked with an asterisk are part of the M-Coffee8 selection of methods. Column 2 indicates the average performance of each individual method on HOMSTRAD. Columns 3–7 are the weights for each method as calculated by the indicated weighting schemes. The last two lines show the average score of M-Coffee15 and M-Coffee8, using all the indicted weighting schemes.