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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Figure 2

Evolutionary rate estimation as “curve fitting.”

An example from HIV-1 polymerase gene alignment for which the inferred 7 non-synonymous rate classes. The idealized biological rate distribution (unobservable) is depicted by the dashed line. The goodness of fit, the complexity of the models, and the range of maximum likelihood parameter estimates are listed in the table.

Figure 2