Fig. 1

Comparison of accuracy of phylogenetic reconstruction. For model trees of 16, 32, 64, 128, and 256 taxa, ancestral sequences of 250, 500, 750, and 1000 amino acids in length were randomly generated under the following conditions: the probability of amino acid substitutions was fixed at 0.01 per site per branch, and the probabilities of insertion and deletion changes were changed to a 0.001, b 0.002 and c 0.005 per site per branch. The accuracy of phylogenetic reconstruction was evaluated as the percentage of replications in which the correct topology was obtained when compared to the model tree