Analyses of substitution saturation at each codon position. Maximum likelihood saturation plots  were compared (a) between the complete amino-acid and nucleotide datasets, and (b) between the codon positions of the complete nucleotide dataset. The observed pairwise distances between the 16 taxa were directly computed from sequence alignments, and the corresponding inferred pairwise tree distances calculated from branch lengths of the ML topology. The Y = × line marks the theoretical limit where the number of observed substitutions equals the number of inferred substitutions. The slope of the linear regression indicates the amount of substitution saturation; the smaller the slope, the greater the number of inferred multiple substitutions.
Chiari et al. BMC Biology 2012 10:65 doi:10.1186/1741-7007-10-65