A new linear-time heuristic algorithm for computing the parsimony score of phylogenetic networks: Theoretical bounds and empirical performance

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Phylogenies play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks, rather than trees, of relationships. In a series of papers, we have extended the maximum parsimony (MP) criterion to phylogenetic networks, demonstrated its appropriateness, and established the intractability of the problem of scoring the parsimony of a phylogenetic network. In this work we show the hardness of approximation for the general case of the problem, devise a very fast (linear-time) heuristic algorithm for it, and implement it on simulated as well as biological data.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - Third International Symposium, ISBRA 2007, Proceedings
PublisherSpringer Verlag
Pages61-72
Number of pages12
ISBN (Print)3540720308, 9783540720300
DOIs
StatePublished - 2007
Externally publishedYes
Event3rd International Symposium Bioinformatics Research and Applications, ISBRA 2007 - Atlanta, GA, United States
Duration: 7 May 200710 May 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4463 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference3rd International Symposium Bioinformatics Research and Applications, ISBRA 2007
Country/TerritoryUnited States
CityAtlanta, GA
Period7/05/0710/05/07

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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