Skip to main content
SpringerLink
Log in
Book cover

Encyclopedia of Algorithms pp 1–6Cite as

Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

  • Living reference work entry
  • First Online:

  • 569 Accesses

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...

This is a preview of subscription content, log in via an institution.

Recommended Reading

  1. Atteson K (1999) The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25:251–278

    Article  MathSciNet  MATH  Google Scholar 

  2. Bordewich M, Gascuel O, Huber KT, Moulton V (2009) Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans Comput Biol Bioinformatics 6:110–117

    Article  Google Scholar 

  3. Bordewich M, Mihaescu R (2013) Accuracy guarantees for phylogeny reconstruction algorithms based on balanced minimum evolution. IEEE/ACM Trans Comput Biol Bioinformatics 10:576–583

    Article  Google Scholar 

  4. Brown DG, Truszkowski J (2012) Fast phylogenetic tree reconstruction using locality-sensitive hashing. Algorithms in bioinformatics. Springer, Berlin/Heidelberg, pp 14–29

    Google Scholar 

  5. Dai W, Xu Y, Zhu B (2006) On the edge l∞ radius of Saitou and Nei’s method for phylogenetic reconstruction. Theor Comput Sci 369:448–455

    Article  MathSciNet  Google Scholar 

  6. Desper R, Gascuel O (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum- evolution principle. J Comput Biol 9:687–706

    Article  Google Scholar 

  7. Elias I, Lagergren J (2005) Fast neighbor joining. In: Proceedings of the 32nd international colloquium on automata, languages, and programming (ICALP), Lisbon, pp 1263–1274

    Google Scholar 

  8. Evans J, Sheneman L, Foster J (2006) Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J Mol Evol 62:785–792

    Article  Google Scholar 

  9. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland

    Google Scholar 

  10. Gascuel O, McKenzie A (2004) Performance analysis of hierarchical clustering algorithms. J Classif 21:3–18

    Article  MathSciNet  MATH  Google Scholar 

  11. Gascuel O, Steel M (2006) Neighbor-joining revealed. Mol Biol Evol 23:1997–2000

    Article  Google Scholar 

  12. Gascuel O, Steel M (2014) A ‘stochastic safety radius’ for distance-based tree reconstruction. Algorithmica 1–18. http://dx.doi.org/10.1007/s00453-015-0005-y

  13. Gronau I, Moran S (2007) Neighbor joining algorithms for inferring phylogenies via LCA distances. J Comput Biol 14:1–15

    Article  MathSciNet  Google Scholar 

  14. Hein J (1989) An optimal algorithm to reconstruct trees from additive distance data. Bull Math Biol 51:597–603

    Article  MATH  Google Scholar 

  15. Pardi F, Guillemot S, Gascuel O (2010) Robustness of phylogenetic inference based on minimum evolution. Bull Math Biol 72:1820–1839

    Article  MathSciNet  MATH  Google Scholar 

  16. Pauplin Y (2000) Direct calculation of a tree length using a distance matrix. J Mol Evol 51:41–47

    Google Scholar 

  17. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  Google Scholar 

  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    Google Scholar 

  19. Shigezumi T (2006) Robustness of greedy type minimum evolution algorithms. In: Computational science–ICCS, Reading, pp 815–821

    Google Scholar 

  20. Simonsen M, Mailund T, Pedersen CNS (2011) Inference of large phylogenies using neighbour-joining. In: Fred A, Felipe J, Gamboa H (eds) Biomedical engineering systems and technologies. Communications in computer and information science, vol 127. Springer, Berlin/Heidelberg, pp 334–344

    Chapter  Google Scholar 

  21. Willson S (2005) Minimum evolution using ordinary least-squares is less robust than neighbor-joining. Bull Math Biol 67:261–279

    Article  MathSciNet  Google Scholar 

  22. Zarestkii K (1965) Reconstructing a tree from the distances between its leaves. (In Russian) Usp Math Nauk 20:90–92

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut de Biologie Computationnelle, Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), UMR 5506, CNRS & Université de Montpellier, Bâtiment 5, 860 rue de Saint Priest, 34095, Montpellier cedex 5, France

    Olivier Gascuel & Fabio Pardi

  2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK

    Jakub Truszkowski

  3. Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, CB2 0RE, Cambridge, UK

    Jakub Truszkowski

Authors
  1. Olivier Gascuel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fabio Pardi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jakub Truszkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Olivier Gascuel .

Editor information

Editors and Affiliations

  1. Dept. Electrical Engineering & Computer Science, Northwestern University, Evanston, Illinois, USA

    Ming-Yang Kao

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this entry

Cite this entry

Gascuel, O., Pardi, F., Truszkowski, J. (2015). Distance-Based Phylogeny Reconstruction: Safety and Edge Radius. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27848-8_115-2

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-27848-8_115-2

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Online ISBN: 978-3-642-27848-8

  • eBook Packages: Springer Reference Computer SciencesReference Module Computer Science and Engineering

Publish with us

Policies and ethics

Search

Navigation