Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time
A phylogenetic network is a rooted acyclic digraph whose leaves are labeled with a set of taxa. The tree containment problem is a fundamental problem arising from model validation in the study of phylogenetic networks. It asks to determine whether or not a given network displays a given phylogenetic tree over the same leaf set. It is known to be NP-complete in general. Whether or not it remains NP-complete for stable networks is an open problem. We make progress towards answering that question by presenting a quadratic time algorithm to solve the tree containment problem for a new class of networks that we call genetically stable networks, which include tree-child networks and comprise a subclass of stable networks.
The project was financially supported by Merlion Programme 2013.
- 3.Gambette, P., Gunawan, A.D.M., Labarre, A., Vialette, S., Zhang, L.: Locating a tree in a phylogenetic network in quadratic time. In: Przytycka, T.M. (ed.) RECOMB 2015. LNCS, vol. 9029, pp. 96–107. Springer, Heidelberg (2015)Google Scholar
- 4.Gusfield, D.: ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, Cambridge (2014)Google Scholar