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

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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

images\ebx_-265033088.gif

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

images\ebx_-2001353100.gif

Variances

images\ebx_795891365.gif

where

images\ebx_-1614287287.gif

 

See also Nei and Kumar (2000), page 40.