Kimura gamma distance

Kimura’s two-parameter gamma model corrects for multiple hits, taking into account transition A transition occurs when a purine is substituted by a purine, or a pyrimidine by a pyrimidine.RH_Transitional and transversion A change from a purine to a pyrimidine, or vice versa, is a transversion.RH_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 According to the gamma distribution, the substitution rate often varies from site to site within a sequence. The shape of this distribution is determined by a value known as the gamma parameter, which is also known as the shape parameter.RH_Gamma_parameter for computing this distance.

The Kimura 2-parameter model

MEGA provides facilities for computing the following quantities:

The formulas for computing these quantities are as follows:

Distances

where P and Q are the respective total frequencies of transition A transition occurs when a purine is substituted by a purine, or a pyrimidine by a pyrimidine. type pairs and transversion A change from a purine to a pyrimidine, or vice versa, is a 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.