Inferring phylogenetic relationships avoiding forbidding rooted triplets

Ying Jun He, Trinh N.D. Huynh, Jesper Andreas Jansson, Wing Kin Sung

Research output: Journal article publicationJournal articleAcademic researchpeer-review

18 Citations (Scopus)

Abstract

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set C and none of the rooted triplets in another given set F. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.
Original languageEnglish
Pages (from-to)59-74
Number of pages16
JournalJournal of Bioinformatics and Computational Biology
Volume4
Issue number1
DOIs
Publication statusPublished - 3 Apr 2006
Externally publishedYes

Keywords

  • Algorithm
  • Galled network
  • NP-hardness
  • Phylogenetic network construction
  • Rooted triplet

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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