Pamilo-Bianchi-Li Method

This method (Pamilo and Bianchi 1993; Li 1993) is a modification of Li, Wu and Luo's method. The only difference concerns the allocation of 2-fold sites to synonymous and nonsynonymous categories. Rather than assuming an equal transition and transversion rate, the rate is inferred from the observed number of transitions and transversions at the 4-fold degenerate sites. Based on this information, the following quantities can be estimated:

Synonymous distance

This is the number of synonymous substitutions per synonymous site.

Nonsynonymous distance

This is the number of nonsynonymous substitutions per nonsynonymous site.

 Substitutions at the 4-fold degenerate sites (d4)

This is the number of substitutions per 4-fold degenerate site; it is useful for measuring the rate of neutral evolution.

 Substitutions at the 0-fold degenerate sites (d0)

This is the number of substitutions per 0-fold degenerate site; it is useful for measuring the rate of amino acid sequence evolution.

 Number of 4-fold degenerate sites(L4)

The estimate of the number of 4-fold degenerate sites, computed by averaging the number of 4-fold degenerate sites in the two sequences, compared.

 Number of 0-fold degenerate sites (L0)

The estimate of the number of 0-fold degenerate sites, computed by averaging the number of 0-fold degenerate sites in the two sequences, compared.

Difference between synonymous and nonsynonymous distances (D)

This computes the differences between the synonymous and nonsynonymous distances. These statistics are useful for conducting tests of selection.

The formulas for computing these quantities are:

Here,

are the number of 0-fold, 2-fold and 4-fold degenerate sites, respectively.

, and

, where

, , ,

Pi and Qi are the proportions of i-fold degenerate sites that show transitional and transversional differences, respectively.

,

See also Nei and Kumar (2000), page 64.