Jukes-Cantor distance

In the Jukes and Cantor (1969)Jukes_and_Cantor_1969 model, the rate of nucleotide substitution is the same for all pairs of the four nucleotides A, T, C, and G.  As is shown below, the multiple hit correction equation for this model produces a maximum likelihood estimate of the number of nucleotide substitutions between two sequences.  It assumes an equality of substitution rates among sites (see the related gamma distanceHC_Jukes_Cantor_Gamma_distance), equal nucleotide frequencies, and it does not correct for higher rate of transition A transition occurs when a purine is substituted by a purine, or a pyrimidine by a pyrimidine.RH_Transitional substitutions as compared to transversion A change from a purine to a pyrimidine, or vice versa, is a transversion.RH_Transversional substitutions.

The Jukes-Cantor model

MEGA provides facilities for computing the following quantities:

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

where p is the proportion of sites with different nucleotides.

Variance

See also Nei and Kumar (2000)Nei_and_Kumar_2000, page 36.