Example phylogenetic tree (for 12 Hepatitis B Virus strains). The (unrooted) tree is used to select a list of sequence pairs tracing round the outside of the tree. For this tree, the 12 sequence pairs would be reference - X70185, X70185 - D00329, D00329 - woodchuck, woodchuck - monkey, monkey - X75663, X75663 - X02496, X02496 - X75664, X75664 - AB056514, AB056514 - X75665, X75665 - AB074755, AB074755 - D50520 and D50520 - reference. Note that this set of pairwise comparisons covers each branch of the tree precisely twice - hence no branch is given more weight than another. In general, the set of pairs selected in this way is not unique - e.g. branches of the tree may be flipped into different places without changing the phylogeny.

In MLOGD, as well as calculating nucleotide-by-nucleotide MLOGD scores for each reference sequence - non-reference sequence pair, scores are also calculated for each of the pairs tracing round the tree, and summed up over all pairs to give a phylogenetically-summed MLOGD score. In fact the sum is then divided by two (since each branch is covered twice by the above pairs) and then divided by two again (since for each pair A - B, both A versus B and B versus A MLOGD scores are calculated; the two scores may differ slightly due to the treatment of gaps etc.).