Kimura’s two-parameter gamma model corrects for multiple hits, taking into account transition al and transversion al substitution rates and differences in substitution rates among sites. Evolutionary rates among sites are modeled using the Gamma distribution, and you will need to provide a gamma parameter for computing this distance.
The Kimura 2-parameter model
MEGA provides facilities for computing the following quantities:
Quantity |
Description |
d: Transitions + Transversions |
Number of nucleotide substitutions per site. |
s: Transitions only |
Number of transitional substitutions per site. |
v: Transversions only |
Number of transversional substitutions per site. |
R = s/v |
Transition /transversions ratio. |
L: No of valid common sites |
Number of sites compared. |
The formulas for computing these quantities are as follows:
Distances
where P and Q are the respective total frequencies of transition type pairs and transversion type pairs, a is the gamma parameter, and
Variances
where
See also Nei and Kumar (2000), page 44 and estimating gamma parameter.