In computational
phylogenetics
In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
, generalized tree alignment is the problem of producing a
multiple sequence alignment and a
phylogenetic tree
A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...
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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