No. of differences (Amino acids)

This distance is the number of sites at which two sequences being compared are different. If the sequences contain alignment gaps or missing data and you are using the pairwise deletion option, you must realize that this count does not normalize the number of differences based on the number of valid sites compared. Therefore, if you use this distance, we recommend that you use the complete-deletion option.

MEGA computes the following quantities:

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

The formulas used are:

Quantity	Formula	Variance
$image\ndiffsaa_d1.gif$	None	$image\ndiffsaa_d2.gif$