Generalized tree alignment

From HandWiki

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 S and an edit distance function d between sequences,

Output: A tree T leaf-labeled by S and labeled with sequences at the internal nodes, such that Σe∈Td(e) is minimized, where d(e) is the edit distance between the endpoints of e.[2]

Note that this is in contrast to tree alignment, where the tree is provided as input.

References

  1. ↑ Schwikowski, Benno; Vingron, Martin (1997). "The Deferred Path Heuristic for the Generalized Tree Alignment Problem". Journal of Computational Biology 4 (3): 415–431. doi:10.1089/cmb.1997.4.415. ISSN 1066-5277. PMID 9278068. 
  2. ↑ Srinivas Aluru (21 December 2005). Handbook of Computational Molecular Biology. CRC Press. pp. 19–26. ISBN 978-1-4200-3627-5. https://books.google.com/books?id=3Ss-ws2Zm6IC&pg=SA19-PA27. 



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