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Approximation algorithms for the fixed-topology phylogenetic number problem

By Mary Cryan, Leslie Ann Goldberg and Cynthia A. Phillips

Abstract

In the l-phylogeny problem, one wishes to construct an evolutionary tree for a. set of species represented by characters, in which each state of each character induces no more than l connected components. We consider the fixed-topology version of this problem for fixed-topologies of arbitrary degree. This version of the problem is known to be NP-complete for l greater than or equal to 3 even for degree-3 trees in which no state labels more than l + 1 leaves (and therefore there is a trivial l + 1 phylogeny) We give a 2-approximation algorithm for all l greater than or equal to 3 for arbitrary input topologies and we give an optimal approximation algorithm that constructs a 4-phylogeny when a 3-phylogeny exists. Dynamic programming techniques, which are typically used in fixed-toplogy problems, cannot be applied to l-phylogeny problems. Our 2-approximation algorithm is the first application of linear programming to approximation algorithms for phylogeny problems. We extend our results to a related problem in which characters are polymorphic

Topics: QA76
Publisher: Springer Berlin Heidelberg
Year: 1997
OAI identifier: oai:wrap.warwick.ac.uk:11855
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