Constructing Level-2 Phylogenetic Networks from Triplets

L. Van Iersel, J. Keijsper, S. Kelk, L. Stougie, F. Hagen, T. Boekhout

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)667-681
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume6
Issue number4
DOIs
Publication statusPublished - 1 Oct 2009

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