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Accuracy Guarantees for Phylogeny Reconstruction Algorithms Based on Balanced Minimum Evolution

  • Magnus Bordewich
  • Radu Mihaescu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)

Abstract

Distance based phylogenetic methods attempt to reconstruct an accurate phylogenetic tree relating a given set of taxa from an estimated matrix of pair-wise distances between taxa. This paper examines two distance based algorithms (GreedyBME and FastME) which are based on the principle of trying to minimise the balanced minimum evolution (BME) score of the output tree in relation to the given estimated distance matrix. We show firstly that these algorithms will both reconstruct the correct tree if the input data is quartet consistent, and secondly that if the maximum error in any individual distance estimate is ε, then both algorithms will output trees containing all edges of the true tree that have length at least 3ε. That is to say the algorithms have edge safety radius 1/3. In contrast, quartet consistency of the data is not sufficient to guarantee Neighbor Joining (NJ) reconstructs the correct tree, and moreover NJ has edge safety radius of 1/4, which is strictly worse.

Keywords

Maximum Error Neighbor Join Correct Tree True Tree Pendent Edge 
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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References

  1. 1.
    Atteson, K.: The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251–278 (1999)CrossRefGoogle Scholar
  2. 2.
    Bordewich, M., Gascuel, O., Huber, K., Moulton, V.: Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(1), 110–117 (2009)CrossRefPubMedGoogle Scholar
  3. 3.
    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)CrossRefPubMedGoogle Scholar
  4. 4.
    Desper, R., Gascuel, O.: Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle. J. Comp. Biol. 9, 587–598 (2002), Latest software available at, http://atgc.lirmm.fr/fastme/
  5. 5.
    Desper, R., Gascuel, O.: Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21, 587–598 (2004)CrossRefPubMedGoogle Scholar
  6. 6.
    Felsenstein, J.: An alternating least-squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46, 101–111 (1997)CrossRefPubMedGoogle Scholar
  7. 7.
    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)CrossRefPubMedGoogle Scholar
  8. 8.
    Gascuel, O., Steel, M.: Neighbor-joining revealed. Mol. Biol. Evol. 23(11), 1997–2000 (2006)CrossRefPubMedGoogle Scholar
  9. 9.
    Hordijk, W., Gascuel, O.: Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 21(24), 4338–4347 (2005)CrossRefPubMedGoogle Scholar
  10. 10.
    Mihaescu, R.: Reliability results for the general Balanced Minimum Evolution principle (in preparation)Google Scholar
  11. 11.
    Mihaescu, R., Levy, D., Pachter, L.: Why neighbor-joining works. Algorithmica 54(1), 1–24 (2009)CrossRefGoogle Scholar
  12. 12.
    Pardi, F., Guillemot, S., Gascuel, O.: Robustness of phylogenetic inference based on minimum evolution. Bulletin of Mathematical Biology (2010) (in press)Google Scholar
  13. 13.
    Pauplin, Y.: Direct calculation of tree length using a distance matrix. J. Mol. Evol. 51, 66–85 (2000)CrossRefGoogle Scholar
  14. 14.
    Saitou, N., Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–424 (1987)PubMedGoogle Scholar
  15. 15.
    Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)Google Scholar
  16. 16.
    Shigezumi, T.: Robustness of greedy type minimum evolution algorithms. In: Computational Science –ICCS 2006, pp. 815–821 (2006)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Magnus Bordewich
    • 1
  • Radu Mihaescu
    • 2
  1. 1.School of Engineering and Computing SciencesDurham UniversityU.K.
  2. 2.Dept. of Computer ScienceU. C. BerkeleyU.S.A.

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