Python package of codon usage bias analysis tools

BayesCode, a Bayesian framework for phylogenetic comparative methods and phylogenetic codon models

MATLAB package for codon usage bias and NGS analysis

a demonstration of Godon usage; Godon is implementing codon model optimization written in Go

An improved codon modeling approach for accurate estimation of the mutation bias

Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution