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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.

From: Ancestral sequence alignment under optimal conditions

Data Set Gap Scaling Method Parsimony Ambiguous Parsimony ML Ambiguous ML
Early Growth Max 86.92% 85.07% 86.59% 86.13%
  Expected 89.95% 89.79% 89.17% 89.31%
Early Growth Double Length Max 66.10% 64.51% 67.17% 66.10%
  Expected 71.12% 73.48% 72.02% 73.81%
Late Growth Max 95.02% 95.21% 93.52% 92.31%
  Expected 96.04% 96.35% 95.03% 94.68%
Late Growth Double Length Max 85.95% 86.39% 82.74% 75.98%
  Expected 88.38% 89.91% 87.17% 85.35%