rbcL dataset: Comparison of all models presented in this paper to the GTR model, when treating each codon position separately. The performance of "traditional" codon partition models (up to the dotted horizontal line) can be improved significantly by assuming context-dependent evolution at the third codon position. As is confirmed in this figure, such context-dependent codon partition models systematically outperform the (independent) codon partition models in terms of model fit. Further, the models that assume that first and second codon positions evolve according to a separately evolutionary model (in this figure) systematically outperform those models that treat first and second codon positions identically (from an evolutionary perspective).
Baele et al. BMC Evolutionary Biology 2011 11:145 doi:10.1186/1471-2148-11-145