Fig. 6

Equilibrium frequency inference error with a strongly non-ultrametric tree. a: The strongly non-ultrametric phylogenetic tree under which simulations for this figure are performed. Some tips of the tree (e.g. T10, T20) are close to the root while others (T1, T11) are considerably more evolutionarily distant; in an ultrametric tree, all tips would instead have the same distance from the root. b and c: Violin plots summarising nucleotide frequency inference error (y-axis), measured as the Euclidean distance between the vectors of column-specific simulated nucleotide frequencies and inferred ones. Each plot contains 10 replicates, and each replicate contains (b) 800 alignment columns evolved under the background nucleotide frequencies, or (c) 200 alignment columns evolved under equilibrium nucleotide frequencies sampled from a Dirichlet distribution with \(\alpha =0.1\). Each plot refers to a particular character frequency inference method, indicated on the x-axis