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.
|Journal||IEEE/ACM Transactions on Computational Biology and Bioinformatics|
|Publication status||Published - 1 Oct 2009|
Van Iersel, L., Keijsper, J., Kelk, S., Stougie, L., Hagen, F., & Boekhout, T. (2009). Constructing Level-2 Phylogenetic Networks from Triplets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4), 667-681. https://doi.org/10.1109/TCBB.2009.22