The performance of ML tree reconstruction with the JTT + F + Γ model and the JTT + cF + Γ model. The data were simulated under the site-specific frequency model (JTT + ssF + Γ) based on amino acid frequencies observed at each site of the HSP90 alignment. The ranges of branch-lengths a and b are 0.05–1.45 and 0.5–2.95, respectively, with an increment of 0.05. The left and right heatmaps represent, respectively, the proportions of correctly estimated trees estimated under JTT + F + Γ and JTT + cF + Γ models. Each box of the heatmaps represents 100 simulations for the given conditions.