Living Reference Work Entry

Encyclopedia of Algorithms

pp 1-6

Date: Latest Version

Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

  • Olivier GascuelAffiliated withInstitut de Biologie Computationnelle, Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), UMR 5506, CNRS & Université de Montpellier Email author 
  • , Fabio PardiAffiliated withInstitut de Biologie Computationnelle, Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), UMR 5506, CNRS & Université de Montpellier
  • , Jakub TruszkowskiAffiliated withEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusCancer Research UK Cambridge Institute, University of Cambridge

Keywords

Phylogeny reconstruction Distance methods Performance analysis Robustness Safety radius approach Optimal radius

Years and Authors of Summarized Original Work

  • 1999; Atteson

  • 2005; Elias, Lagergren

  • 2006; Dai, Xu, Zhu

  • 2010; Pardi, Guillemot, Gascuel

  • 2013; Bordewich, Mihaescu

Problem Definition

A phylogeny is an evolutionary tree tracing the shared history, including common ancestors, of a set of extant species or “taxa.” Phylogenies are increasingly reconstructed on the basis of molecular data (DNA and protein sequences) using statistical techniques such as likelihood and Bayesian methods. Algorithmically, these techniques suffer from the discrete nature of tree topology space. Since the number of tree topologies increases exponentially as a function of the number of taxa, and each topology requires a separate likelihood calculation, it is important to restrict the search space and to design efficient heuristics. Distance methods for phylogeny reconstruction serve this purpose by inferring trees in a fraction of the time required for the more statistically rigorous methods. Distance methods also provide fa ...

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