Fig. 5

Equilibrium frequency inference error under different scenarios. Similarly to Fig. 4, we compare the accuracy of different methods for reconstructing equilibrium frequencies. However, here we consider the simulation scenarios of amino acid sequences and modified trees with increased over-representation of human sequences. Values shown are as in Fig. 4. Each plot contains 10 replicates, and each replicate contains 800 alignment columns evolved under the background character frequencies (a, c and e), or 200 alignment columns evolved under equilibrium character frequencies sampled from a Dirichlet distribution with \(\alpha =0.1\) for d and f and \(\alpha =0.02\) for b. In a and b simulations are under the tree in Fig. 1 and with amino acid sequences. In c and d we consider nucleotide sequences and the tree in Fig. 1 with 100 added human sequences (see Methods). In e and f we instead add 1000 human sequences. Results from additional methods (e.g. Bayesian approaches) are shown in Additional file 1: Fig. S5. Results from PhyML are not available, due to excessive computational demand