Figure 3.

Example of codons where the posterior p-values under the mixture of codon models differs significantly from p-values obtained from the conditional p-value method. Amino acids V,A,G,D,L do not have any common properties, so, under the codon mixture model, the column is assigned to a functional class with little selective pressure, explaining why the p-value produced for the first codon position is small. In contrast, under the conditional p-value approach, the amino acids almost completely determine the first codon position (the only exception being the Fugu codon, encoding a leucine, which could have used a T at the first position), so a poor p-value is reported.

Chen and Blanchette BMC Evolutionary Biology 2007 7(Suppl 1):S9   doi:10.1186/1471-2148-7-S1-S9