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 language | English (US) |
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Pages (from-to) | 675-679 |
Number of pages | 5 |
Journal | Journal of Molecular Evolution |
Volume | 41 |
Issue number | 5 |
DOIs | |
State | Published - Nov 1995 |
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