Kimura 2-parameter distance

Kimura’s two parameter model (1980) corrects for multiple hits, taking into account transitional and 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 distance).

The Kimura 2-parameter model

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MEGA 4 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

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

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Variances

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where

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