Applications of codon and rate variation models in molecular phylogeny

Eric E. Schadt, Janet S. Sinsheimer, Kenneth Lange

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


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 β-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 LINNAEU'S, which is tuned for performance and modeling flexibility.

Original languageEnglish
Pages (from-to)1550-1562
Number of pages13
JournalMolecular Biology and Evolution
Issue number9
StatePublished - 1 Sep 2002
Externally publishedYes


  • Alignment
  • DNA sequence
  • Dynamic programming
  • Evolution
  • Markov chain
  • Markov random field
  • Maximum likelihood


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