One of the simplest estimations of genetic distance is based on the proportion of shared alleles (Bowcock et al. 1994). This distance measure can be calculated between individuals or between populations (Chakraborty and Jin, 1993). For individual pairwise comparisons the proportion of shared alleles is estimated by
where the number of shared alleles S is sumed over all loci u.
Distance between individuals (
) is estimated by,
This individual measure can be used to look at population
substructure. Bowcock et al. (1994) constructed dendrograms
based on 
calculated from human microsatellite data. Using
this technique a correlation between genetic similarity and geographic
location was noted. This distance measure has also proven very
successful at placing unknown individuals into the correct
subpopulation (Estoup et al.
1995b).
If the population subdivison is known then the distance between
populations (
), adjusted for within population variation, can be
calculated by,
where the average proportion of shared alleles between and within populations 1 and 2
(
respectively) is computed overall
possible combinations of individuals sampled.
A second method of estimating distance was developed by Cavalli-Sforza
and Edwards (1967). This method involves the transformation of the
data into an angular distance 
. In this case the populations are
conceptualised as existing as points in a m-dimensional Euclidean
space which are specified by m allele frequencies (i.e. m equals
the total number of alleles in both populations). The distance, 
, is
the angle between these points where,
and 
and 
are the frequencies of the ith allele in
populations x and y respectively. From this a Chord distance
, the distance in the space between the two points measured
along a straight line, is calculated from
This measure is in units of gene substitutions where a value of 1 indicates the complete fixation of alternate alleles in each population. The distance for all loci combined is estimated from Pathagoras' theorem, in that the squared distance of all loci combined is equal to the sum of the squared distance for each locus.
The most commonly used distance measure was developed by Nei (1987).
Nei's standard genetic distance 
is calculated from
where I is a measure of genetic identity. Identity is estimated from
where Jxy, Jx and Jy are the means for all loci of 
,
, and
for each locus.