Encyclopedia of Algorithms

Living Edition
| Editors: Ming-Yang Kao

Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

Living reference work entry
DOI: https://doi.org/10.1007/978-3-642-27848-8_115-2

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...


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

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Olivier Gascuel
    • 1
  • Fabio Pardi
    • 1
  • Jakub Truszkowski
    • 2
    • 3
  1. 1.Institut de Biologie Computationnelle, Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM)UMR 5506, CNRS & Université de MontpellierMontpellier cedex 5France
  2. 2.European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusHinxton, CambridgeUK
  3. 3.Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK