# Tamura-Nei distance

The Tamura-Nei model (1993) corrects for multiple hits, taking into account the differences in substitution rate between nucleotides and the inequality of nucleotide frequencies. It distinguishes between transitional substitution rates between purines and transversional substitution rates between pyrimidines. It also assumes equality of substitution rates among sites (see related gamma model).

The Tamura-Nei model

MEGA 4 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.

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, and

Variances

where