The ultrametric constraint and its application to phylogenetics

Moore, N.C.A. and Prosser, P. (2008) The ultrametric constraint and its application to phylogenetics. Journal of Artificial Intelligence Research, 32, pp. 901-938. (doi: 10.1613/jair.2580)

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A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called supertrees, whilst respecting the relationships in the original trees. A rooted tree exhibits an ultrametric property; that is, for any three leaves of the tree it must be that one pair has a deeper most recent common ancestor than the other pairs, or that all three have the same most recent common ancestor. This inspires a constraint programming encoding for rooted trees. We present an efficient constraint that enforces the ultrametric property over a symmetric array of constrained integer variables, with the inevitable property that the lower bounds of any three variables are mutually supportive. We show that this allows an efficient constraint-based solution to the supertree construction problem. We demonstrate that the versatility of constraint programming can be exploited to allow solutions to variants of the supertree construction problem.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Prosser, Dr Patrick
Authors: Moore, N.C.A., and Prosser, P.
College/School:College of Science and Engineering > School of Computing Science
Journal Name:Journal of Artificial Intelligence Research
Journal Abbr.:J. artif. intell. res.
Publisher:AAAI Press
ISSN (Online):1943-5037

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