For each adjacent pair of haplotypes, x and y, on a network, we estimate the nucleotide diversity, dxy by:

model

where

E is the number of enzyme classes examined
Se is the mean number of restriction sites present in haplotypes x and y for the enzyme class e
re is the length of the recognition sequence of the e-th enzyme class
dxy(e) is the fraction of nucleotide substitutions per site between sequences x and y, estimated for the enzyme class e.

The distance metric becomes

model

where M is the total number of mutational events.
The branch lengths are now instead of 1.