Generalized tree alignment

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 {\displaystyle S} and an edit distance function d {\displaystyle d} between sequences,

Output: A tree T {\displaystyle T} leaf-labeled by S {\displaystyle S} and labeled with sequences at the internal nodes, such that Σ e ∈ T d ( e ) {\displaystyle \Sigma _{e\in T}d(e)} is minimized, where d ( e ) {\displaystyle d(e)} is the edit distance between the endpoints of e {\displaystyle 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.
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