Tree alignment

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

S{displaystyle S}

of sequences, a phylogenetic tree

T{displaystyle T}

leaf-labeled by

S{displaystyle S}

and an edit distance function

d{displaystyle d}

between sequences.

Output: A labeling of the internal vertices of

T{displaystyle T}

such that

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

is minimized, where

d(e){displaystyle d(e)}

is the edit distance between the endpoints of

e{displaystyle e}


The task is NP-hard.[1]

. . . Tree alignment . . .

This article is issued from web site Wikipedia. The original article may be a bit shortened or modified. Some links may have been modified. The text is licensed under “Creative Commons – Attribution – Sharealike” [1] and some of the text can also be licensed under the terms of the “GNU Free Documentation License” [2]. Additional terms may apply for the media files. By using this site, you agree to our Legal pages . Web links: [1] [2]

. . . Tree alignment . . .