Table 3 Alignment accuracies using different gap open cost scaling functions. Alignment accuracies using two different gap cost scaling functions. The unsealed gap open cost is 7 and the unsealed gap extension cost is 1. The Max method scales gap open costs according to the maximum value in the scoring matrix. The Expected method scales gap open costs according to the expected score of a related symbol pair from the two ancestral sequences.
Data Set | Gap Scaling Method | Parsimony | Ambiguous Parsimony | ML | Ambiguous ML |
|---|---|---|---|---|---|
Early Growth | Max | 86.92% | 85.07% | 86.59% | 86.13% |
| Â | Expected | 89.95% | 89.79% | 89.17% | 89.31% |
Early Growth Double Length | Max | 66.10% | 64.51% | 67.17% | 66.10% |
| Â | Expected | 71.12% | 73.48% | 72.02% | 73.81% |
Late Growth | Max | 95.02% | 95.21% | 93.52% | 92.31% |
| Â | Expected | 96.04% | 96.35% | 95.03% | 94.68% |
Late Growth Double Length | Max | 85.95% | 86.39% | 82.74% | 75.98% |
| Â | Expected | 88.38% | 89.91% | 87.17% | 85.35% |