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
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), page 37.