Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.

  title={Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.},
  author={Rasmus Nielsen and Zamin Yang},
  volume={148 3},
Several codon-based models for the evolution of protein-coding DNA sequences are developed that account for varying selection intensity among amino acid sites. The "neutral model" assumes two categories of sites at which amino acid replacements are either neutral or deleterious. The "positive-selection model" assumes an additional category of positively selected sites at which nonsynonymous substitutions occur at a higher rate than synonymous ones. This model is also used to identify target… CONTINUE READING
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