Codon model of amino acid toggling.
The immune escape and reversion model has three classes of codons: codons encoding the wild type amino acid (class x); codons separated from the wild type by a single nucleotide substitution (y); and codons separated from the wild type by more than one substitution (z). In the example shown, phenylalanine (F) is the wild type amino acid. Rates of substitution between F and each of the six amino acids within one nucleotide substitution of F or from these amino acids back to F are affected by the parameter ρ, the amino acid toggling rate. All other non-synonymous substitutions have a multiplier ω instead of ρ. Rates of all substitutions depend on the frequency parameters , where c represents the codon class. The parameters take account of the codon bias estimated across the entire alignment and free parameters tc which describe the proportion of time spent by the site in each of the three codon classes.