The Tamura-Nei model (1993) corrects for multiple hits, taking into account the substitution rate differences between nucleotides and the inequality of nucleotide frequencies. It distinguishes between transitional substitution rates between purines and transversional substitution rates between pyrimidines. It assumes an equality of substitution rates among sites (see related gamma model).When nucleotide frequencies are different between the sequences, the modified formula (Tamura and Kumar 2002) relaxes the assumption of substitution pattern homogeneity.
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. |
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, gXA, gXC, gXG, gXT, are the respective frequencies of A, C, G and T of sequence X, gXR = gXA + gXG and gXY = gXT + gXC, gA, gC, gG, gT, gR, and gY are the average frequencies of the pair of sequences, and
The variances can be estimated by the bootstrap method.