Scoring Metrics

There are several known useful possibilities for measuring the divergence of a set of aligned strings, namely the total distance between them.

• Distance from Consensus - The consensus of an alignment is a string of the most common character in each column of the alignment. The total distance between the strings is defined as the number of characters that differ from the consensus character of their column.
• Evolutionary Tree Alignment - The weight of the lightest evolutionary tree that can be constructed from the sequences, with the weight of the tree defined as the number of changes between pairs of sequences that correspond to two adjacent nodes in the tree, summed over all such pairs.
• Sum of Pairs - The sum of pairwise distances between all the pairs of sequences.