Dinneen, MJGhodla, PSLinz, S2023-01-242023-01-242022CDMTCS Research Reports CDMTCS-560 (2022)1178-3540https://hdl.handle.net/2292/62555to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze phylogenetic networks, the problem of deciding whether or not a given rooted phylogenetic network embeds a given rooted phylogenetic tree is of recurring interest. This problem, formally know as Tree Containment, is NP-complete in general and polynomial-time solvable for certain classes of phylogenetic networks. In this paper, we connect ideas from quantum computing and phylogenetics to present an efficient Quadratic Unconstrained Binary Optimization formulation for Tree Containment in the general setting. For an instance (N, T ) of Tree Containment, where N is a phylogenetic network with nN vertices and T is a phylogenetic tree with nT vertices, the number of logical qubits that are required for our formulation is O(nNnT ).Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htmTechnical ReportFields of ResearchCopyright: The author(s)http://purl.org/eprint/accessRights/OpenAccess