Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Abstract

Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these models are almost always estimated using nucleotide frequencies observed in a sequence alignment, primarily as a matter of historical… (More)
DOI: 10.1371/journal.pone.0011230

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