title: Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites.
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(-2d)/2d, 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 + 2d)]/2d accounts for the general case where substitution rates can differ for both amino acids and sites.
authors.affiliation: Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX, 75235, USA.
authors.forename: N V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D019943:Amino Acid Substitution; D019143:Evolution, Molecular; D008957:Models, Genetic; D016012:Poisson Distribution