CodonTest: modeling amino acid substitution preferences in coding sequences.

ABSTRACT: 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 estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we d

SUBMITTER: Delport W 

PROVIDER: S-EPMC2924240 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature