A cubic-time algorithm for computing the trinet distance between level-1 networks

Moulton, Vincent, Oldman, James and Wu, Taoyang (2017) A cubic-time algorithm for computing the trinet distance between level-1 networks. Information Processing Letters, 123. 36–41. ISSN 0020-0190

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    Abstract

    In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have efficiently computable metrics with which to systematically compare such networks. Through developing an optimal algorithm to enumerate all trinets displayed by a level-1 network (a type of network that is slightly more general than an evolutionary tree), here we propose a cubic-time algorithm to compute the trinet distance between two level-1 networks. Employing simulations, we also present a comparison between the trinet metric and the so-called Robinson-Foulds phylogenetic network metric restricted to level-1 networks. The algorithms described in this paper have been implemented in JAVA and are freely available at (https://www.uea.ac.uk/computing/TriLoNet)

    Item Type: Article
    Uncontrolled Keywords: phylogenetic tree,phylogenetic network,level-1 network,trinet,robinson-foulds metric
    Faculty \ School: Faculty of Science > School of Computing Sciences
    University of East Anglia > Faculty of Science > Research Groups > Computational Biology (subgroups are shown below) > Computational biology of RNA
    University of East Anglia > Faculty of Science > Research Groups > Computational Biology (subgroups are shown below) > Phylogenetics
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    Depositing User: Pure Connector
    Date Deposited: 14 Mar 2017 01:41
    Last Modified: 25 Jul 2018 13:24
    URI: https://ueaeprints.uea.ac.uk/id/eprint/62948
    DOI: 10.1016/j.ipl.2017.03.002

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