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Generalized tree alignment
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In computational phylogenetics, generalized tree alignment is the problem of producing a multiple sequence alignment and a phylogenetic tree 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.