atpB dataset: Comparison of all models presented in this paper to the GTR model, when grouping the first and second codon positions together. 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 can be seen from this figure, such context-dependent codon partition models systematically outperform the (independent) codon partition models in terms of model fit.
Baele et al. BMC Evolutionary Biology 2011 11:145 doi:10.1186/1471-2148-11-145