Note that this still does not correct for differences in the rates of
transition and transversion. To do this you can use what is called the
Kimura 2-parameter correction. This was a method established by Kimura
(1980; J.Mol.Evol. 16:111-120) where the rates of transitions are
assumed to be 
and the rates of transversions are 
.
Then if the observed number of transitional differences are P and the
observed number of transversion differences are Q, the estimate of
distance is
and
where 
, 
and 
. Again divergence follows a logarithmic
function.
In this case you can also determine the rates of substitution via transitions and transversions separately. The rate of transition substitutions per site is
where 
. The rate of transversion
substitutions per site is
