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.[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.


  1. ^ Schwikowski, Benno; Vingron, Martin (1997). "The Deferred Path Heuristic for the Generalized Tree Alignment Problem". Journal of Computational Biology. 4 (3): 415–431. ISSN 1066-5277. doi:10.1089/cmb.1997.4.415. 
  2. ^ Srinivas Aluru (21 December 2005). Handbook of Computational Molecular Biology. CRC Press. pp. 19–26. ISBN 978-1-4200-3627-5.