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....


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

  1. 1.
    Atteson, K.: The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251–278 (1999)MathSciNetzbMATHCrossRefGoogle Scholar
  2. 2.
    Bruno, W.J., Socci, N.D., Halpern, A.L.: Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol. 17, 189–197 (2000)CrossRefGoogle Scholar
  3. 3.
    Desper, R., Gascuel, O.: Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum – Evolution Principle. J. Comput. Biol. 9, 687–706 (2002)CrossRefGoogle Scholar
  4. 4.
    Elias, I. Lagergren, J.: Fast Neighbor Joining. In: Proceedings of the 32nd International Colloquium on Automata, Languages, and Programming (ICALP), pp. 1263–1274 (2005)Google Scholar
  5. 5.
    Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts (2004)Google Scholar
  6. 6.
    Gascuel, O.: BIONJ: an Improved Version of the NJ Algorithm Based on a Simple Model of Sequence Data. Mol. Biol. Evol. 14, 685–695 (1997)CrossRefGoogle Scholar
  7. 7.
    Gascuel, O. McKenzie, A.: Performance Analysis of Hierarchical Clustering Algorithms. J. Classif. 21, 3–18 (2004)zbMATHCrossRefGoogle Scholar
  8. 8.
    Gascuel, O., Steel, M.: Neighbor-Joining Revealed. Mol. Biol. Evol. 23, 1997–2000 (2006)CrossRefGoogle Scholar
  9. 9.
    Huson, D.H., Nettles, S., Warnow, T.: Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6, 369–386 (1999)CrossRefGoogle Scholar
  10. 10.
    Jukes, T.H., Cantor, C.R.: Evolution of Protein Molecules. In: Munro, H.N. (ed.), Mammalian Protein Metabolism, pp. 21–132, Academic Press, New York (1969)Google Scholar
  11. 11.
    Saitou, N., Nei, M.: The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol. 4, 406–425 (1987)Google Scholar
  12. 12.
    Vinh, L.S., von Haeseler, A.: Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinformatics 6, 92 (2005)CrossRefGoogle Scholar
  13. 13.
    Zarestkii, K.: Reconstructing a tree from the distances between its leaves. Uspehi Mathematicheskikh Nauk 20, 90–92 (1965) (in russian)Google Scholar

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