p-distance (Nucleotide)

This distance is the proportion (p) of nucleotide sites at which two sequences being compared are different. It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared.  It does not make any correction for multiple substitutions at the same site, substitution rate biases (for example, differences in the transitionalRH_Transition and transversionalRH_Transversion rates), or differences in evolutionary rates among sites.

MEGA provides facilities for computing following p-distances and related quantities:

d: Transitions + Transversions  : Proportion of nucleotide sites that are different.

s: Transitions only : Proportion of nucleotide sites with transitional differences.

v: Transversions only : Proportion of nucleotide sites with transversional differences.

R = s/v : Transition A transition occurs when a purine is substituted by a purine, or a pyrimidine by a pyrimidine./transversions ratio.

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

Formulas for computing these quantities are as follows:

p,  n_d/L, p(1 – p)/L

s, p, s(1 – s)/L

v, Q, v(1 – v)/L

R, P/Q, [c₁²P + c₂²Q – (c₁P + c₂Q)²)]/L

where c₁ = 1/s and c₂ = -s/v²

P and Q are the proportion of sites showing transitional and transversional differences, respectively.

See also Nei and Kumar (2000)Nei_and_Kumar_2000, page 33.