Orienting undirected phylogenetic networks

Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yuki Murakami, Charles Semple

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Abstract

This paper studies the relationship between undirected (unrooted) and directed
(rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network N can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of N and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well studied class of binary tree-child networks satisfies these conditions.
Original languageEnglish
Article number103480
JournalJournal of Computer and System Sciences
Volume140
Early online date4 Oct 2023
DOIs
Publication statusPublished - Mar 2024

Keywords

  • phylogenetic network
  • graph orientation
  • graph algorithm
  • fixed-parameter tractability
  • polynomial-time algorithm
  • characterization
  • computational biology
  • phylogenetics

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