CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

  title={CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences},
  author={Wayne Delport and Konrad Scheffler and Gordon Botha and Michael B. Gravenor and Spencer V. Muse and Sergei L. Kosakovsky Pond},
  booktitle={PLoS Computational Biology},
Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their… CONTINUE READING
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