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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Figure 4

Evolutionary rate clusters in structured GA models () inferred from the HIV-1 group M pol alignment.

Each cluster is labeled with the maximum likelihood estimate of its rate inferred under . The residues (nodes) are annotated by their biochemical properties and Stanfel class, and the rates (edges) are labeled with model-averaged () rate estimates. The style of an edge is determined by its cluster affinity, where high cluster affinities indicate that a large proportion of models in the credible set were consistent with the structured model.

Figure 4