Kimura gamma distance

Kimuras two-parameter gamma model corrects for multiple hits, taking into account transitional and transversional 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

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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

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where P and Q are the respective total frequencies of transition type pairs and transversion type pairs, a is the gamma parameter, and

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Variances

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where

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See also Nei and Kumar (2000), page 44 and estimating gamma parameter.