Figure 4.

atpB dataset: Estimated substitution patterns for the independent evolutionary models at first, second and third codon positions and the context-dependent evolutionary model at the third codon position for the GTR₁₂₃+Γ₁₂₃+CP₁₂₃+F₁₂₃+FF₁₆+3F model. At the left of this figure, i.e. the first two columns, the independent model estimates for first (1^st CP), second (2^nd CP) and third (3^rd CP) codon positions are shown. At the right of the figure (columns 3 through 10), the context-dependent estimates for the third codon position are shown for each evolutionary context, i.e. each neighbouring base combination. In the figure, the substitution parameter types (i.e. rAG, rAC, ..., rTC) each have a unique colour, as indicated in the legend panel within the figure, and the same colour is used for every model (context-dependent or not).