Computing the maximum agreement of phylogenetic networks

  • Authors:

  • Charles Choy;Jesper Jansson;Kunihiko Sadakane;Wing-Kin Sung

  • Affiliations:

  • School of Computing, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore;School of Computing, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore;Department of Computer Science and Communication Engineering, Kyushu University, Japan;School of Computing, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore

  • Venue:
  • Theoretical Computer Science - Pattern discovery in the post genome
  • Year:
  • 2005

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Abstract

We introduce the maximum agreement phylogenetic subnetwork problem (MASN) for finding branching structure shared by a set of phylogenetic networks. We prove that the problem is NP-hard even if restricted to three phylogenetic networks and give an O(n2)-time algorithm for the special case of two level-1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a level-f phylogenetic network if every biconnected component in the underlying undirected graph induces a subgraph of N containing at most f nodes with indegree 2. We also show how to extend our technique to yield a polynomial-time algorithm for any two level-f phylogenetic networks N1, N2 satisfying f = O(log n); more precisely, its running time is O(|V (N1)| ċ |V (N2)| ċ 2f1 + f2), where V (Ni) and fi denote the set of nodes in Ni and the level of Ni, respectively, for i ∈ {1, 2}.