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Constructing Level-2 Phylogenetic Networks from Triplets

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6 Author(s)
van Iersel, L. ; Dept. of Math. & Stat., Univ. of Canterbury, Christchurch, New Zealand ; Keijsper, J. ; Kelk, S. ; Stougie, L.
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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. 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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Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:6 ,  Issue: 4 )