In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree, modeling the evolutionary relationships between species or taxa. The edit distances between sequences are calculated for each of the tree’s internal vertices, such that the sum of all edit distances within the tree is minimized. Tree alignment can be accomplished using one of several algorithms with various trade-offs between manageable tree size and computational effort.

 This article needs attention from an expert in Computational Biology. (November 2018)

## . . . Tree alignment . . .

Input: A set

${displaystyle S}$

of sequences, a phylogenetic tree

${displaystyle T}$

leaf-labeled by

${displaystyle S}$

and an edit distance function

${displaystyle d}$

between sequences.

Output: A labeling of the internal vertices of

${displaystyle T}$

such that

${displaystyle Sigma _{ein T}d(e)}$

is minimized, where

${displaystyle d(e)}$

is the edit distance between the endpoints of

${displaystyle e}$

.