Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
Baele, Guy Van de Peer, Yves × Vansteelandt, Stijn #
BMC Evolutionary Biology vol:11 pages:145
Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a viable alternative, mimicking the substitution behaviour of codon models at a low computational cost. Such codon partition models however impose independent evolution of the different codon positions, which is overly restrictive from a biological point of view. Given that empirical research has provided indications of context-dependent substitution patterns at four-fold degenerate sites, we take those indications into account in this paper.