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Constructing the Simplest Possible Phylogenetic Network from Triplets

Leo van IerselContact Information and Steven KelkContact Information

(4)  Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
(5)  Centrum voor Wiskunde en Informatica (CWI), P.O. Box 94079, 1090 GB Amsterdam, The Netherlands
Abstract
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest possible phylogenetic network consistent with an input set T, where T contains at least one phylogenetic tree on three leaves (a triplet) for each combination of three taxa. To quantify the complexity of a network we consider both the total number of reticulations and the number of reticulations per biconnected component, called the level of the network. We give polynomial-time algorithms for constructing a level-1 respectively a level-2 network that contains a minimum number of reticulations and is consistent with T (if such a network exists). In addition, we show that if T is precisely equal to the set of triplets consistent with some network, then we can construct such a network, which minimises both the level and the total number of reticulations, in time O(|T| k + 1), if k is a fixed upper bound on the level.
Part of this research has been funded by the Dutch BSIK/BRICKS project.

Contact Information Leo van Iersel
Email: l.j.j.v.iersel@tue.nl

Contact Information Steven Kelk
Email: s.m.kelk@cwi.nl
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