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Reconstructing One-Articulated Networks with Distance Matrices

  • Kuang-Yu Chang
  • Yun Cui
  • Siu-Ming Yiu
  • Wing-Kai HonEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10330)

Abstract

Given a distance matrix M that represents evolutionary distances between any two species, an edge-weighted phylogenetic network N is said to satisfy M if between any pair of species, there exists a path in N with length equal to the corresponding entry in M. In this paper, we consider a special class of networks called 1-articulated network which is a proper superset of galled trees. We show that if the distance matrix M is derived from an ultrametric 1-articulated network N (i.e., for any species X and Y, the entry M(XY) is equal to the shortest distance between X and Y in N), we can re-construct an network that satisfies M in \(O(n^2)\) time, where n denotes the number of species; furthermore, the reconstructed network is guaranteed to be the simplest, in a sense that the number of hybrid nodes is minimized. In addition, one may easily index a 1-articulated network N with minimum number of hybrid nodes in O(n) space, such that on given any phylogenetic tree T, we can determine if T is contained in N (i.e., if a spanning subtree \(T'\) of N is a subdivision of T) in O(n) time.

Keywords

Distance Matrix Edge Weight Evolutionary Path Phylogenetic Network Split Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Kuang-Yu Chang
    • 1
  • Yun Cui
    • 2
  • Siu-Ming Yiu
    • 2
  • Wing-Kai Hon
    • 1
    Email author
  1. 1.National Tsing Hua UniversityHsinchuTaiwan
  2. 2.The University of Hong KongPokfulamHong Kong

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