Figure 2

Mixture of codon substitution models based on amino acid functionality classes. (Top) Stationary distributions estimated from the Pfam database for the 50 functional classes. Each row corresponds to one class. The numbers on the right are the prior probability of each class. (Bottom) Two examples of codon rates matrices, where dark cells correspond to high substitution rates and light cells to low rates. The left matrix corresponds to a functional class that favors hydrophobic residues (ILV), while the right matrix comes from a class that favors the glycine amino acid (G).