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Molecular Biology and Evolution 19:1550-1562 (2002)
© 2002 Society for Molecular Biology and Evolution

Applications of Codon and Rate Variation Models in Molecular Phylogeny

Eric E. Schadt*{dagger}, Janet S. Sinsheimer*{ddagger} and Kenneth Lange*{ddagger}

*Department of Biomathematics, UCLA School of Medicine, Los Angeles;
{dagger}Department of Computational Genomics, Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, Washington;
{ddagger}Department of Human Genetics, UCLA School of Medicine, Los Angeles

The current article illustrates the practical advantages of some new models and statistical algorithms for codon substitution and spatial rate variation in molecular phylogeny. Our companion paper in this issue discusses at length the mathematical properties of these models for nucleotide and codon substitution, for site-to-site and branch-to-branch heterogeneity in rates of evolution, and for spatial correlation in the assignment of rates. In this study we summarize the theoretical background and apply the models and algorithms to data on ß-globin, the complete HIV genome, and the mitochondrial genome. Our complex but realistic models enhance biological interpretation of sequence data and show substantial improvements in model fit over existing models. All the new statistical algorithms applied are incorporated in our phylogeny software LINNAEUS, which is tuned for performance and modeling flexibility.


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E. Schadt and K. Lange
Codon and Rate Variation Models in Molecular Phylogeny
Mol. Biol. Evol., September 1, 2002; 19(9): 1534 - 1549.
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