Modeling evolution at the protein level using an adjustable amino acid fitness model

An adjustable fitness model for amino acid site substitutions is investigated. This model, a generalization of previously developed evolutionary models, has several distinguishing characteristics: it separately accounts for the processes of mutation and substitution, allows for heterogeneity among substitution rates and among evolutionary constraints, and does not make any prior assumptions about which sites or characteristics of proteins are important to molecular evolution. While the model has fewer adjustable parameters than the general reversible mtREV model, when optimized it outperforms mtREV in likelihood analysis on protein-coding mitochondrial genes. In addition, the optimized fitness parameters of the model show correspondence to some biophysical characteristics of amino acids.