Skip to main content
SpringerLink
Log in

Fast Error-Tolerant Quartet Phylogeny Algorithms

  • Conference paper
Combinatorial Pattern Matching (CPM 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6661))

Included in the following conference series:

Abstract

We present a quartet-based phylogeny algorithm that returns the correct topology for n taxa in O(n logn) time with high probability, assuming each quartet is inconsistent with the true tree topology with constant probability, independent of other quartets. Our incremental algorithm relies upon a search tree structure for the phylogeny that is balanced, with high probability, no matter the true topology. In experiments, our prototype was as fast as the fastest heuristics, but because real data do not typically satisfy our probabilistic assumptions, its overall performance is not as good as our theoretical results predict.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., Sonnhammer, E.L.L.: The Pfam protein families database. Nucleic Acids Research 30(1), 276–280 (2002)

    Article  Google Scholar 

  2. Berry, V., Jiang, T., Kearney, P.E., Li, M., Wareham, H.T.: Quartet cleaning: Improved algorithms and simulations. In: Nešetřil, J. (ed.) ESA 1999. LNCS, vol. 1643, pp. 313–324. Springer, Heidelberg (1999)

    Google Scholar 

  3. Brodal, G., Fagerberg, R., Pedersen, C.: Computing the quartet distance between evolutionary trees in time O(n log n). Algorithmica 38, 377–395 (2003)

    Article  MATH  Google Scholar 

  4. Bryant, D., Tsang, J., Kearney, P.E., Li, M.: Computing the quartet distance between evolutionary trees. In: Proceedings of SODA 2000, pp. 285–286 (2000)

    Google Scholar 

  5. Csűrös, M.: Fast recovery of evolutionary trees with thousands of nodes. J. Comp. Biol. 9(2), 277–297 (2002)

    Article  Google Scholar 

  6. Daskalakis, C., Mossel, E., Roch, S.: Phylogenies without branch bounds: Contracting the short, pruning the deep. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 451–465. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  7. Dubhashi, D.P., Panconesi, A.: Concentration of measure for the analysis of randomized algorithms. Cambridge Univ. Press, Cambridge (2009)

    Book  MATH  Google Scholar 

  8. Erdös, P.L., Steel, M.A., Székely, L.A., Warnow, T.: A few logs suffice to build (almost) all trees: Part II. Theor. Comput. Sci. 221(1-2), 77–118 (1999)

    Article  MATH  Google Scholar 

  9. Feige, U., Peleg, D., Raghavan, P., Upfal, E.: Computing with unreliable information. In: Proceedings of STOC 1990, pp. 128–137.

    Google Scholar 

  10. Felsenstein, J.: Inferring Phylogenies. Sinauer (2001)

    Google Scholar 

  11. Gronau, I., Moran, S., Snir, S.: Fast and reliable reconstruction of phylogenetic trees with very short edges. In: Proceedings of SODA 2008, pp. 379–388 (2008)

    Google Scholar 

  12. Jiang, T., Kearney, P., Li, M.: Orchestrating quartets: Approximation and data correction. In: Proceedings of FOCS 1998, pp. 416–425 (1998)

    Google Scholar 

  13. Kannan, S.K., Lawler, E.L., Warnow, T.J.: Determining the evolutionary tree using experiments. J. Algorithms 21(1), 26–50 (1996)

    Article  MathSciNet  MATH  Google Scholar 

  14. Kao, M.Y., Lingas, A., Östlin, A.: Balanced randomized tree splitting with applications to evolutionary tree constructions. In: Meinel, C., Tison, S. (eds.) STACS 1999. LNCS, vol. 1563, pp. 184–196. Springer, Heidelberg (1999)

    Chapter  Google Scholar 

  15. Karp, R.M., Kleinberg, R.: Noisy binary search and its applications. In: Proceedings of SODA 2007, pp. 881–890 (2007)

    Google Scholar 

  16. King, V., Zhang, L., Zhou, Y.: On the complexity of distance-based evolutionary tree reconstruction. In: Proceedings of SODA 2003, pp. 444–453 (2003)

    Google Scholar 

  17. Price, M.N., Dehal, P.S., Arkin, A.P.: FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 26(7), 1641–1650 (2009)

    Article  Google Scholar 

  18. Ranwez, V., Gascuel, O.: Quartet-based phylogenetic inference: Improvements and limits. Molecular Biology and Evolution 18(6), 1103–1116 (2001)

    Article  MATH  Google Scholar 

  19. Snir, S., Warnow, T., Rao, S.: Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm. Journal of Computational Biology 15(1), 91–103 (2008)

    Article  MathSciNet  Google Scholar 

  20. Sonnhammer, E.L.L., Hollich, V.: Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinformatics 6, 108 (2005)

    Article  Google Scholar 

  21. Strimmer, K., von Haeseler, A.: Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. E 13(7), 964–969 (1996)

    Article  Google Scholar 

  22. Wu, G., Kao, M.Y., Lin, G., You, J.H.: Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability. Alg. Mol. Biol. 3 (2008)

    Google Scholar 

  23. Wu, G., You, J.H., Lin, G.: Quartet-based phylogeny reconstruction with answer set programming. IEEE/ACM Trans. Comput. Biol. Bioinf. 4(1), 139–152 (2007)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canada

    Daniel G. Brown & Jakub Truszkowski

Authors
  1. Daniel G. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jakub Truszkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Mathematics, Università degli Studi di Palermo, Via Archirafi 34, 90123, Palermo, Italy

    Raffaele Giancarlo

  2. Department of Computer Science, University of ’Piemonte Orientale’, Viale T. Michel 11, 15121, Alessandria, Italy

    Giovanni Manzini

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Brown, D.G., Truszkowski, J. (2011). Fast Error-Tolerant Quartet Phylogeny Algorithms. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21458-5_14

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-21458-5_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21457-8

  • Online ISBN: 978-3-642-21458-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation