p-distance (Amino acids)

This distance is the proportion (p) of amino acid sites at which the two sequences to be compared are different. It is obtained by dividing the number of amino acid differences by the total number of sites compared. It does not make any correction for multiple substitutions at the same site or differences in evolutionary rates among sites.

MEGA provides facilities to compute the following quantities:

Quantity	Description
d: distance	Proportion of amino acid sites different.
L: No of valid common sites	Number of sites compared.

The formulas used are:

Quantity	Formula	Variance
$image\pdistaa_d1.gif$	$image\pdistaa_d2.gif$	$image\pdistaa_d3.gif$

where $image\pdistaa_d4.gif$ is the number of amino acids that are different between two aligned sequences.