Tree Containment With Soft Polytomies

Matthias Bentert (1) , Josef Malík (2) , Mathias Weller (3)

1 TU - Technical University of Berlin / Technische Universität Berlin
2 CTU - Czech Technical University in Prague
3 LIGM - Laboratoire d'Informatique Gaspard-Monge

The Tree Containment problem has many important applications in the study of evolutionary history. Given a phylogenetic network N and a phylogenetic tree T whose leaves are labeled by a set of taxa, it asks if N and T are consistent. While the case of binary N and T has received considerable attention, the more practically relevant variant dealing with biological uncertainty has not. Such uncertainty manifests itself as high-degree vertices (" polytomies ") that are " jokers " in the sense that they are compatible with any binary resolution of their children. Contrasting the binary case, we show that this problem, called Soft Tree Containment, is N P-hard, even if N is a binary, multi-labeled tree in which each taxon occurs at most thrice. On the other hand, we reduce the case that each label occurs at most twice to solving a 2-SAT instance of size O(|T|^3).

Domaines: Bio-informatique [q-bio.QM]; Algorithme et structure de données [cs.DS]

Matthias Bentert, Josef Malík, Mathias Weller. Tree Containment With Soft Polytomies. SWAT 2018, Jun 2018, Malmö, Sweden. pp.9:1-9:14. ⟨hal-01734619⟩