Kimura 2-parameter distance

Kimura’s two parameter model (1980Kimura_1980) corrects for multiple hits, taking into account transitionRH_Transitional and transversionRH_Transversional substitution rates, while assuming that the four nucleotide frequencies are the same and that rates of substitution do not vary among sites (see related Gamma distanceHC_Kimura_2_parameter_Gamma_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.

Formulas for computing these quantities are as follows:

Distances

where P and Q are the frequencies of sites with transitional and transversional differences respectively, and

Variances

where

 

See also Nei and Kumar (2000)Nei_and_Kumar_2000, page 37.