In computational
phylogenetics, generalized tree alignment is the problem of producing a
multiple sequence alignment and a
phylogenetic tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
on a set of sequences simultaneously, as opposed to separately.
Formally, Generalized tree alignment is the following optimization problem.
Input: A set
and an edit distance function
between sequences,
Output: A tree
leaf-labeled by
and labeled with sequences at the internal nodes, such that
is minimized, where
is the edit distance between the endpoints of
.
Note that this is in contrast to
tree alignment, where the tree is provided as input.
References
Computational phylogenetics
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