Nei-Gojobori Method

This method computes the numbers of synonymous and nonsynonymous substitutions and the numbers of potentially synonymous and potentially nonsynonymous sites (Nei and Gojobori 1986). Based on these estimates, MEGA can be asked to produce the following quantities:

 

Number of differences (Sd or Nd)

These are simple counts of the number 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 possible number of 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 the synonymous and nonsynonymous distances. These statistics are useful in conducting tests for selection.

 

 Number of Sites (S or N)

The numbers of potential 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:

 

Quantity

Formula

Variance

image\neigojometh_d1.gif

image\neigojometh_d5.gif

image\neigojometh_d11.gif

image\neigojometh_d2.gif

image\neigojometh_d6.gif

image\neigojometh_d12.gif

image\neigojometh_d3.gif

image\neigojometh_d7.gif

image\neigojometh_d13.gif

image\neigojometh_d4.gif

image\neigojometh_d8.gif

image\neigojometh_d14.gif

Dp

image\neigojometh_d9.gif

image\neigojometh_d15.gif

Dd

image\neigojometh_d10.gif

image\neigojometh_d16.gif

 

See also Nei and Kumar (2000), page 52