The network is used to find distances between pairs of haplotypes. A suitable network is a minimum spanning tree.

The observed haplotypes occur at the nodes of the network, not just at the tips as in other sorts of trees.

Assumptions

The probability of a transformation from state 1 to state 0 in some small unit of evolutionary time is equivalent to that of a change from state 0 to state 1.
For example, the probability of a restriction loss equals the probability of a restriction site gain.
Mutational events are independent and equally important.

Additional Criteria

When several connections of equal length are possible for a particular haplotype

a link between two rare haplotypes is less likely than a link between rare and frequent haplotypes;
links between haplotypes that are found within the same population or the same region are favoured over links between types from different regions.

If *pj is the vector of mutational changes for haplotype j, then the distance between haplotypes j and k is:

model

where W = I implies the second assumption above.