The authors suggested alternative ways of accommodating nucleotide/codon frequencies in models of codon substitution.
Selective pressure was evaluated using the probabilistic Markov models of codon substitution [27], [28].
Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution.
First, the HyPhy package [22] was used for fitting distinct models of codon substitution [23], [24], on a full-likelihood Neighbor Joining tree.
This program works by assessing the fit of the data to various models of codon evolution while taking into account the phylogenetic relationships of the sequences.
We applied models of codon evolution which allow for variation in dN/dS among codons but assume the same distribution in all branches of the phylogeny.
Some have attempted to incorporate amino acid substitution biases into models of codon evolution and have shown improved model performance versus the single rate model.
When developing multi-rate models of codon evolution we should strive to not only beat the single-rate model, but also to approximate the REV model with the fewest possible parameters.
Our current work is focussed on inferring multi-rate models of codon evolution from alignments, and in particular the development of a Genetic Algorithm [18] for multi-rate codon model selection.
Models of codon evolution have proven useful for investigating the strength and direction of natural selection.
Maximum likelihood models of codon substitution account for variable selective pressures among amino acid sites.
