Tajima-Nei distance

In real data, nucleotide frequencies often deviate substantially from 0.25. In this case the Tajima-Nei distance (Tajima and Nei 1984) gives a better estimate of the number of nucleotide substitutions than the Jukes-Cantor distance. Note that this assumes an equality of substitution rates among sites and between transitional and transversional substitutions.

The Felsenstein-Tajima-Nei model

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MEGA provides facilities for computing the following quantities for this method:

d: Transitions + Transversions : Number of nucleotide substitutions per site.

L: No of valid common sites: Number of sites compared.

Formulas for computing these quantities are as follows:

Distance

$image\ebx_1353172486.gif$

where p is the proportion of sites with different nucleotides and

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where xij is the relative frequency of the nucleotide pair i and j, gis are the nucleotide frequencies.

Variance

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