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Table 1 Alignment accuracies using correct gap costs. Alignment accuracies using a gap open cost of 7 and the optimal gap extension cost of 0.57. P-values are computed using a paired Student's t-test.

From: Ancestral sequence alignment under optimal conditions

Data Set Measure Parsimony Ambiguous Parsimony ML Ambiguous ML Ma et al. ClustalW
Early Growth Mean 88.43% 83.83% 87.86% 86.26% 91.74% 91.25%
  Std. 2.89% 5.94% 2.79% 4.27% 1.69% 2.28%
  P-value 1.6461 × 10-65 1.1992 × 10-17 N/A
Early Growth Double Length Mean 64.68% 57.24% 63.54% 59.89% 74.29% 72.35%
  Std. 5.23% 8.25% 4.99% 7.59% 4.62% 4.30%
  P-value 1.5922 × 10-103 1.9161 × 10-21 N/A
Late Growth Mean. 95.76% 96.01% 89.44% 87.52% 96.63% 96.79%
  Std 1.29% 1.28% 5.44% 7.03% 0.99% 1.10%
  P-value 7.7818 × 10-10 1.0404 × 10-12 N/A
Late Growth Double Length Mean 86.71% 88.12% 64.76% 55.67% 89.68% 89.54%
  Std. 2.71% 2.85% 7.94% 12.62% 2.42% 2.11%
  P-value 2.1699 × 10-43 2.5033 × 10-50 N/A