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Issue No. 04 - October-December (2009 vol. 6)
ISSN: 1545-5963
pp: 667-681
Leo van Iersel , University of Canterbury, Christchurch
Judith Keijsper , Technische Universiteit Eindhoven, Eindhoven
Steven Kelk , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
Leen Stougie , Centrum voor Wiskunde en Informatica (CWI) and Free University, Amsterdam
Ferry Hagen , Centraalbureau voor Schimmelcultures (CBS), Utrecht
Teun Boekhout , Centraalbureau voor Schimmelcultures (CBS), Utrecht
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.
Phylogenetic networks, level-2, triplets, reticulations, polynomial time algorithms.

L. Stougie, L. van Iersel, T. Boekhout, S. Kelk, J. Keijsper and F. Hagen, "Constructing Level-2 Phylogenetic Networks from Triplets," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. , pp. 667-681, 2009.
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