The analysis of molecular variance is performed using the distances between pairs of haplotypes as data , and with W as a weight matrix, as follows.

Distance can be defined in a variety of ways.

Euclidean distance-- a simple count of the number of differences between two haplotypes.
All haplotypes are equidistant. They are merely recorded as being different or the same.
Distance is measured along a network.
Distance is measured along a network but the distances are weighted according to the nucleotide diversity between adjacent types in the network.

Unweighted Euclidean and network distance metrics are best understood by way of an illustration.

AMOVA is not strictly rigorous with a non-Euclidean metric.