Generalized tree alignment explained
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.[1]
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
.
[2] Note that this is in contrast to tree alignment, where the tree is provided as input.
Notes and References
- Schwikowski. Benno. Vingron. Martin. The Deferred Path Heuristic for the Generalized Tree Alignment Problem. Journal of Computational Biology. 4. 3. 1997. 415–431. 1066-5277. 10.1089/cmb.1997.4.415. 9278068.
- Book: Srinivas Aluru. Handbook of Computational Molecular Biology. 21 December 2005. CRC Press. 978-1-4200-3627-5. 19–26. Srinivas Aluru.