Abstract
INTRODUCTIONPhylogenetic analysis of a multiple sequence alignment (msa) can be performed using distance methods, which are based on genetic distances between sequence pairs in an msa. The genetic distance between two sequences is the fraction of aligned positions in which the sequence has been changed. In contrast, sequence identity is the fraction of the aligned positions that are identical. Gaps may be ignored in distance calculations or treated like substitutions. A scoring or substitution matrix may also be used, making the calculation slightly more complicated, although the principle is the same. Sequence pairs that have the smallest distances are "neighbors." On a tree, these sequences share a node or common ancestor position and are each joined to that node by a branch.
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