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Table 2 Alignment accuracies for differing gap open costs. Alignment accuracies for various gap open costs using a gap extension cost of 0.57.

From: Ancestral sequence alignment under optimal conditions

Data Set Gap Open Cost Parsimony Ambiguous Parsimony ML Ambiguous ML Ma et al. ClustalW
Early Growth 5 89.27% 88.41% 88.43% 88.09% 92.77% 90.48%
  7 88.43% 83.83% 87.86% 86.26% 91.74% 91.25%
  9 86.17% 76.04% 86.13% 82.58% 90.42% 91.48%
  Change 3.10% 12.37% 2.3% 5.51% 2.35% 1.00%
Early Growth Double Length 5 63.43% 63.32% 63.01% 63.05% 78.19% 69.63%
  7 64.68% 57.24% 63.54% 59.89% 74.29% 72.35%
  9 61.40% 46.72% 60.02% 52.33% 68.44% 73.59%
  Change 2.03% 16.6% 2.99% 10.72% 9.75% 3.96%
Late Growth 5 95.95% 96.35% 92.06% 91.70% 96.97% 96.50%
  7 95.76% 96.01% 89.44% 87.52% 96.63% 96.79%
  9 95.21% 95.39% 84.95% 80.71% 96.12% 96.91%
  Change 0.74% 0.96% 7.11% 10.99% 0.85% 0.41%
Late Growth Double Length 5 86.21% 88.91% 73.21% 68.18% 91.43% 88.17%
  7 86.71% 88.12% 64.76% 55.67% 89.68% 89.54%
  9 85.58% 86.16% 54.36% 43.02% 87.08% 90.15%
  Change 0.63% 2.75% 18.85% 25.16% 4.35% 1.98%