Encyclopedia of Algorithms

2008 Edition
| Editors: Ming-Yang Kao

Distance-Based Phylogeny Reconstruction (Optimal Radius)

1999; Atteson2005; Elias, Lagergren
  • Richard Desper
  • Olivier Gascuel
Reference work entry
DOI: https://doi.org/10.1007/978-0-387-30162-4_115

Keywords and Synonyms

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

Problem Definition

A phylogeny is an evolutionary tree tracing the shared history, including common ancestors, of a set of extant taxa. Phylogenies have been historically reconstructed using character-based (parsimony) methods, but in recent years the advent of DNA sequencing, along with the development of large databases of molecular data, has led to more involved methods. Sophisticated techniques such as likelihood and Bayesian methods are used to estimate phylogenies with sound statistical justifications. However, these statistical 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 separate likelihood calculation, it is important to restrict the search space and to design efficient heuristics....

Keywords

Distance Matrix Neighbor Join Distance Method Phylogeny Reconstruction Extant Taxon 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Recommended Reading

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Richard Desper
    • 1
  • Olivier Gascuel
    • 2
  1. 1.Department of BiologyUniversity College LondonLondonUK
  2. 2.LIRMMNational Scientific Research CenterMontpellierFrance