Reconstructing an ultrametric galled phylogenetic network from a distance matrix

Ho Leung Chan, Jesper Andreas Jansson, Tak Wah Lam, Siu Ming Yiu

Research output: Journal article publicationJournal articleAcademic researchpeer-review

16 Citations (Scopus)

Abstract

Given a distance matrix M that specifies the pairwise evolutionary distances between n species, the phylogenetic tree reconstruction problem asks for an edge-weighted phylogenetic tree that satisfies M, if one exists. We study some extensions of this problem to rooted phylogenetic networks. Our main result is an O(n2log n)-time algorithm for determining whether there is an ultrametric galled network that satisfies M, and if so, constructing one. In fact, if such an ultrametric galled network exists, our algorithm is guaranteed to construct one containing the minimum possible number of nodes with more than one parent (hybrid nodes). We also prove that finding a largest possible submatrix M′ of M such that there exists an ultrametric galled network that satisfies M′ is NP-hard. Furthermore, we show that given an incomplete distance matrix (i.e. where some matrix entries are missing), it is also NP-hard to determine whether there exists an ultrametric galled network which satisfies it.
Original languageEnglish
Pages (from-to)807-832
Number of pages26
JournalJournal of Bioinformatics and Computational Biology
Volume4
Issue number4
DOIs
Publication statusPublished - 1 Aug 2006
Externally publishedYes

Keywords

  • Algorithm
  • Distance-based reconstruction
  • Phylogenetic network
  • Ultrametric galled network

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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