Test | Defaults | VTML200 | >Acc | MUSCLE | PROBCONS |
|---|
B3 TC | 44.8% | 48.4% | 8% | 53.2% | 61.3% |
B3 SPS | 78.6% | 80.9% | 3% | 84.4% | 88.3% |
P4 SPS | 61.7% | 64.6% | 5% | 67.7% | 71.7% |
- Improvement in accuracy of CLUSTALW v2.0.9 by using the VTML200 matrix. B3 is BALIBASE v3, P4 is PREFAB v4. TC and SPS are the average fraction of correctly aligned columns and residue pairs, respectively. In PREFAB reference alignments are pair-wise so SPS and TC are equivalent. Defaults is the accuracies using default parameters, VTML200 with that matrix and gap parameters given in the main text, and >Acc is the improvement due to VTML200. Accuracies of the more recent methods MUSCLE v3.7 and PROBCONS v1.12 are given for comparison.
