TY - JOUR

T1 - Constructing Level-2 Phylogenetic Networks from Triplets

AU - Van Iersel, L.

AU - Keijsper, J.

AU - Kelk, S.

AU - Stougie, L.

AU - Hagen, F.

AU - Boekhout, T.

PY - 2009/10/1

Y1 - 2009/10/1

N2 - 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.

AB - 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.

U2 - 10.1109/TCBB.2009.22

DO - 10.1109/TCBB.2009.22

M3 - Article

VL - 6

SP - 667

EP - 681

JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics

JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics

SN - 1545-5963

IS - 4

ER -