Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

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Abstract

A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e−d corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 − e −2 d)/2 d, derived for the case of substitution rates that are site-independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [ln(1 + 2 d)]/2 d accounts for the general case where substitution rates can differ for both amino acids and sites.

Original languageEnglish (US)
Pages (from-to)675-679
Number of pages5
JournalJournal of Molecular Evolution
Volume41
Issue number5
DOIs
StatePublished - Nov 1995

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Keywords

  • Amino acid substitutions
  • Dayhoff et al.'s distance
  • Evolutionary distance
  • Gamma distance
  • PAM scale

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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