Molecular Biology and Evolution, Vol 11, 725-736, Copyright © 1994 by Society for Molecular Biology and Evolution
N Goldman and Z Yang
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 fit to data than can
nucleotide-based models and can produce more reliable estimates of certain
biologically important measures such as the transition/transversion rate
ratio and the synonymous/nonsynonymous substitution rate ratio.
ORIGINAL ARTICLE
A codon-based model of nucleotide substitution for protein-coding DNA sequences
Laboratory of Mathematical Biology, National Institute for Medical Research, United Kingdom.
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C. Greenman, R. Wooster, P. A. Futreal, M. R. Stratton, and D. F. Easton Statistical Analysis of Pathogenicity of Somatic Mutations in Cancer Genetics, August 1, 2006; 173(4): 2187 - 2198. [Abstract] [Full Text] [PDF]
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 G. de Martino, I. Pan, E. Emmanuel, A. Levy, and V. F. Irish Functional Analyses of Two Tomato APETALA3 Genes Demonstrate Diversification in Their Roles in Regulating Floral Development PLANT CELL, August 1, 2006; 18(8): 1833 - 1845. [Abstract] [Full Text] [PDF]
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R. E. Broughton and P. C. Reneau Spatial Covariation of Mutation and Nonsynonymous Substitution Rates in Vertebrate Mitochondrial Genomes Mol. Biol. Evol., August 1, 2006; 23(8): 1516 - 1524. [Abstract] [Full Text] [PDF]
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J. A. Andres, L. S. Maroja, S. M. Bogdanowicz, W. J. Swanson, and R. G. Harrison Molecular Evolution of Seminal Proteins in Field Crickets Mol. Biol. Evol., August 1, 2006; 23(8): 1574 - 1584. [Abstract] [Full Text] [PDF]
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J. B. Plotkin, J. Dushoff, M. M. Desai, and H. B. Fraser Estimating Selection Pressures from Limited Comparative Data Mol. Biol. Evol., August 1, 2006; 23(8): 1457 - 1459. [Abstract] [Full Text] [PDF]
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