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Constructing Level-2 Phylogenetic Networks from Triplets
October-December 2009 (vol. 6 no. 4)
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.

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Index Terms:
Phylogenetic networks, level-2, triplets, reticulations, polynomial time algorithms.
Citation:
Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout, "Constructing Level-2 Phylogenetic Networks from Triplets," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 667-681, Oct.-Dec. 2009, doi:10.1109/TCBB.2009.22
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