ESTIMATION OF THE NUMBER OF AMINO-ACID SUBSTITUTIONS PER SITE WHEN THE SUBSTITUTION RATE VARIES AMONG SITES

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