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Journal of Molecular Evolution

, Volume 41, Issue 5, pp 675–679 | Cite as

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

  • Nick V. Grishin
Articles

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.

Key words

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

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References

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Copyright information

© Springer-Verlag New York Inc 1995

Authors and Affiliations

  • Nick V. Grishin
    • 1
  1. 1.Department of PharmacologyUniversity of Texas Southwestern Medical SchoolDallasUSA

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