Gamma distance (Amino acids)

The Gamma distance improves upon the Poisson correction distance by taking care of the inequality of the substitution rates among sites. For this purpose, you will need to provide the gamma shape parameter (a).

For estimating the Dayhoff distance, use a = 2.25 (see Nei and Kumar [2000], page 21 for details).

For computing Grishins distance, use a = 0.65. 23 (see Nei and Kumar [2000], page 23 for details)

MEGA provides facilities to compute the following quantities:

Quantity	Description
d: distance	Number of amino acid substitutions per site.
L: No of valid common sites	Number of sites compared.

Formulas used are:

Quantity	Formula	Variance
$image\gammadistaa_d1.gif$	$image\gammadistaa_d2.gif$	$image\gammadistaa_d3.gif$

See also Nei and Kumar (2000), page 23 and estimating gamma parameter.