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Table 4 Mean pairwise alignment accuracies using correct gap costs. Mean pairwise 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 95.64% 92.61% 96.19% 95.41% 97.61% 97.48%
  Std. 1.43% 3.47% 1.08% 1.98% 0.48% 0.64%
  P-value 1.3830 × 10-67 9.6503 × 10-17 N/A
Early Growth Double Length Mean 84.33% 78.29% 84.30% 82.19% 91.20% 90.58%
  Std. 2.99% 5.50% 2.91% 4.95% 1.75% 1.51%
  P-value 9.1586 × 10-114 3.5959 × 10-18 N/A
Late Growth Mean 98.13% 98.26% 94.73% 93.74% 98.65% 98.67%
  Std. 0.62% 0.62% 3.14% 4.05% 0.39% 0.44%
  P-value 5.9142 × 10-09 1.1169 × 10-10 N/A
Late Growth Double Length Mean 93.63% 94.45% 80.79% 75.51% 95.50% 95.44%
  Std. 1.37% 1.47% 4.85% 7.91% 1.14% 0.95%
  P-value 2.1676 × 10-44 6.5523 × 10-47 N/A