The Tamura-Nei (1993) distance with the gamma model corrects for multiple hits, taking into account the different rates of substitution between nucleotides and the inequality of nucleotide frequencies. In this distance, evolutionary rates among sites are modeled using the gamma distribution. You will need to provide a gamma parameter for computing this distance.
The Tamura-Nei model
MEGA provides facilities for computing the following quantities for this method:
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 P1 and P2 are the proportions of transitional differences between nucleotides A and G, and between T and C, respectively, Q is the proportion of transversional differences, gA, gC, gG, gT, are the respective frequencies of A, C, G and T, gR = gA + gG, gY, = gT + gC, a is the gamma parameter and
Variances
where
See also Nei and Kumar (2000), page 45 and estimating gamma parameter.