Performance of ML tree reconstructions evaluated using simulations. The performance of ML tree reconstruction with the JTT + F + Γ model for data simulated under (A) the JTT + F + Γ model and (B) under a site-specific frequency model (JTT + ssF + Γ). The site-specific frequency data were derived from the HSP90 data set. The three heatmaps in (A) and (B) represent, respectively, the proportions of "Correct tree" (i.e., taxa 1 and 2 together), "Long branch attracts tree" (i.e., taxa 1 and 3 together) and "Other tree" (i.e., incorrectly put taxa 1 and 4 together) with regard to branch-lengths a and b. The four-taxon tree shown in (A) is the true tree (taxa 1 and 2 together, and taxa 3 and 4 together) used for simulating the data. Each box of the heatmaps represents 100 simulations for the given conditions.