Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
The Structure of Level-k Phylogenetic Networks
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest possible phylogenetic network consistent with an input set T, where T contains at least one phylogenetic tree on three leaves (a triplet) for each combination of three taxa. To quantify the complexity of a network we consider both the total number of reticulations and the number of reticulations per biconnected component, called the level of the network. We give polynomial-time algorithms for constructing a level-1 respectively a level-2 network that contains a minimum number of reticulations and is consistent with T (if such a network exists). In addition, we show that if T is precisely equal to the set of triplets consistent with some network, then we can construct such a network, which minimises both the level and the total number of reticulations, in time O(|T| k + 1), if k is a fixed upper bound on the level.