New results on optimizing rooted triplets consistency

Jaroslaw Byrka, Sylvain Guillemot, Jesper Andreas Jansson

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

3 Citations (Scopus)

Abstract

A set of phylogenetic trees with overlapping leaf sets is consistent if it can be merged without conflicts into a supertree. In this paper, we study the polynomial-time approximability of two related optimization problems called the maximum rooted triplets consistency problem ( ) and the minimum rooted triplets inconsistency problem ( ) in which the input is a set of rooted triplets, and where the objectives are to find a largest cardinality subset of which is consistent and a smallest cardinality subset of whose removal from results in a consistent set, respectively. We first show that a simple modification to Wu's Best-Pair-Merge-First heuristic [25] results in a bottom-up-based 3-approximation for . We then demonstrate how any approximation algorithm for could be used to approximate , and thus obtain the first polynomial-time approximation algorithm for with approximation ratio smaller than 3. Next, we prove that for a set of rooted triplets generated under a uniform random model, the maximum fraction of triplets which can be consistent with any tree is approximately one third, and then provide a deterministic construction of a triplet set having a similar property which is subsequently used to prove that both and are NP-hard even if restricted to minimally dense instances. Finally, we prove that cannot be approximated within a ratio of Ω(logn) in polynomial time, unless P∈=∈NP.
Original languageEnglish
Title of host publicationAlgorithms and Computation - 19th International Symposium, ISAAC 2008, Proceedings
Pages484-495
Number of pages12
DOIs
Publication statusPublished - 1 Dec 2008
Externally publishedYes
Event19th International Symposium on Algorithms and Computation, ISAAC 2008 - Gold Coast, QLD, Australia
Duration: 15 Dec 200817 Dec 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5369 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference19th International Symposium on Algorithms and Computation, ISAAC 2008
CountryAustralia
CityGold Coast, QLD
Period15/12/0817/12/08

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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