Modified Nei-Gojobori Method

The modified Nei-Gojobori distance differs from the original Nei-Gojobori formulation in one way: transitional and transversional substitutions are no longer assumed to occur with the same frequency. Thus the user is requested to provide the Transition/Transversion (R) ratio. When R = 0.5, this method becomes identical to the Nei-Gojobori method. When R > 0.5, the number of synonymous sites is less than estimated using Nei-Gojobori method and consequently, the number of nonsynonymous sites will be larger than estimated with the original Nei-Gojobori (Nei and Gojobori 1986) approach.

Number of differences (Sd or Nd)

These are counts of the numbers of synonymous (Sd) and nonsynonymous (Nd) differences. To compare these two numbers you must use the p-distance because the number of potential synonymous sites is much smaller than the number of nonsynonymous sites.

p-distance (pS or pN)

The count of the number of synonymous differences (Sd) is normalized using the number of potential synonymous sites (S). A similar computation can be made for nonsynonymous differences.

 Jukes-Cantor correction (dS or dN)

The p-distances computed above can be corrected to account for multiple substitutions at the same site.

Difference between synonymous and nonsynonymous distances

MEGA can compute differences between synonymous and nonsynonymous distances. These statistics are useful when conducting tests for selection.

 Number of Sites (S or N)

Numbers of potentially synonymous and nonsynonymous sites can be computed using this option. For each pair of sequences, the average number of synonymous or nonsynonymous sites is reported.

The formulas for computing these quantities are:

See also Nei and Kumar (2000), page 52.