The maximum agreement of two nested phylogenetic networks

Jesper Andreas Jansson, Wing Kin Sung

Research output: Chapter in book / Conference proceedingConference article published in proceeding or bookAcademic researchpeer-review

8 Citations (Scopus)

Abstract

Given a set N of phylogenetic networks, the maximum agreement phylogenetic subnetwork problem (MASN) asks for a subnetwork contained in every Ni∈ N with as many leaves as possible. MASN can be used to identify shared branching structure among phylogenetic networks or to measure their similarity. In this paper, we prove that the general case of MASN is NP-hard already for two phylogenetic networks, but that the problem can be solved efficiently if the two given phylogenetic networks exhibit a nested structure. We first show that the total number of nodes |V(N)| in any nested phylogenetic network N with n leaves and nesting depth d is O(n(d + 1)). We then describe an algorithm for testing if a given phylogenetic network is nested, and if so, determining its nesting depth in O(|V(N)| · (d + 1)) time. Next, we present a polynomial-time algorithm for MASN for two nested phylogenetic networks N1, N2. Its running time is O(|V(N1)| · |V(N2)| · (d1+ 1) · (d2+ 1)), where d1and d2denote the nesting depths of N1and N2, respectively. In contrast, the previously fastest algorithm for this problem runs in O(|V(N1)| · |V(N2)| 4f) time, wheref≥ max{d1, d2}.
Original languageEnglish
Title of host publicationAlgorithms and Computation: 15th International Symposium, ISAAC 2004, Hong Kong, China, December 20-22, 2004. Proceedings
EditorsRudolf Fleischer, Gerhard Trippen
Pages581-593
Number of pages13
Publication statusPublished - 1 Dec 2004
Externally publishedYes
Event15th International Symposium on Algorithms and Computation, ISAAC 2004 - Hong Kong, China
Duration: 20 Dec 200422 Dec 2004

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PublisherSpringer Verlag
VolumeLNCS 3341
ISSN (Print)0302-9743

Conference

Conference15th International Symposium on Algorithms and Computation, ISAAC 2004
CountryChina
CityHong Kong
Period20/12/0422/12/04

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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