Kimura gamma distance

Kimura’s two-parameter gamma model corrects for multiple hits, taking into account transitionRH_Transitional and transversionRH_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 parameterRH_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)Nei_and_Kumar_2000, page 44 and estimating gamma parameterHC_Computing_the_Gamma_Parameter.