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.

## . . . Tree alignment . . .

**Input**: A set

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

such that

${displaystyle Sigma _{ein T}d(e)}$is minimized, where

${displaystyle d(e)}$is the edit distance between the endpoints of

${displaystyle e}$.

The task is NP-hard.[1]

## . . . Tree alignment . . .

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