A codon-based model of nucleotide substitution for protein-coding DNA sequences.

@article{Goldman1994ACM,
  title={A codon-based model of nucleotide substitution for protein-coding DNA sequences.},
  author={N. Goldman and Ziheng Yang},
  journal={Molecular biology and evolution},
  year={1994},
  volume={11 5},
  pages={725-36}
}
A codon-based model for the evolution of protein-coding DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better… CONTINUE READING
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