Skip to main content
SpringerLink
Log in
Book cover

International Symposium on Bioinformatics Research and Applications

ISBRA 2011: Bioinformatics Research and Applications pp 184–196Cite as

Fast Local Search for Unrooted Robinson-Foulds Supertrees

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

Abstract

A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing rooted and unrooted RF supertrees is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted. We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, thereby expanding the utility of RF supertrees. We demonstrate that our local search algorithms yield supertrees with notably better scores than those obtained from rooted heuristics.

This is a preview of subscription content, 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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allen, B.L., Steel, M.: Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics 5, 1–13 (2001)

    Article  MathSciNet  MATH  Google Scholar 

  2. Bansal, M.S., Burleigh, J.G., Eulenstein, O., Fernández-Baca, D.: Robinson-Foulds supertrees. Algorithms for Molecular Biology 5, 18 (2010)

    Article  Google Scholar 

  3. Baum, B.R.: Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3–10 (1992)

    Article  Google Scholar 

  4. Beck, R.M.D., Bininda-Emonds, O.R.P., Cardillo, M., Liu, F.R., Purvis, A.: A higher-level MRP supertree of placental mammals. BMC Evolutionary Biology 6, 93 (2006)

    Article  Google Scholar 

  5. Bender, M.A., Farach-Colton, M.: The LCA problem revisited. In: Gonnet, G.H., Viola, A. (eds.) LATIN 2000. LNCS, vol. 1776, pp. 88–94. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  6. Bininda-Emonds, O.R.P., Beck, R.M.D., Purvis, A.: Getting to the roots of matrix representation. Syst. Biol. 54, 668–672 (2005)

    Article  Google Scholar 

  7. Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., MacPhee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L., Purvis, A.: The delayed rise of present-day mammals. Nature 446, 507–512 (2007)

    Article  Google Scholar 

  8. Bininda-Emonds, O.R.P., Sanderson, M.J.: Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Systematic Biology 50, 565–579 (2001)

    Article  Google Scholar 

  9. Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics 8, 409–423 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  10. Cardillo, M., Bininda-Emonds, O.R.P., Boakes, E., Purvis, A.: A species-level phylogenetic supertree of marsupials. Journal of Zoology 264, 11–31 (2004)

    Article  Google Scholar 

  11. Chen, D., Eulenstein, O., Fernández-Baca, D., Burleigh, J.G.: Improved heuristics for minimum-flip supertree construction. Evolutionary Bioinformatics 2, 347–356 (2006)

    Google Scholar 

  12. Creevey, C.J., McInerney, J.O.: Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21(3), 390–392 (2005)

    Article  Google Scholar 

  13. Davies, T.J., Barraclough, T.G., Chase, M.W., Soltis, P.S., Soltis, D.E., Savolainen, V.: Darwin’s abominable mystery: insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences of the United States of America 101, 1904–1909 (2004)

    Article  Google Scholar 

  14. Eulenstein, O., Chen, D., Burleigh, J.G., Fernández-Baca, D., Sanderson, M.J.: Performance of flip supertree construction with a heuristic algorithm. Systematic Biology 53, 299–308 (2003)

    Article  Google Scholar 

  15. Ganapathy, G., Ramachandran, V., Warnow, T.: Better hill-climbing searches for parsimony. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 245–258. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  16. Ganapathy, G., Ramachandran, V., Warnow, T.: On contract-and-refine transformations between phylogenetic trees. In: SODA, pp. 900–909 (2004)

    Google Scholar 

  17. Goloboff, P.A.: Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15, 415–428 (1999)

    Article  Google Scholar 

  18. Goloboff, P.A.: Minority rule supertrees? MRP, compatibility, and minimum flip display the least frequent groups. Cladistics 21, 282–294 (2005)

    Article  Google Scholar 

  19. Holland, B., Penny, D., Hendy, M.: Outgroup misplacement and phylogenetic inaccuracy under a molecular clock -— a simulation study. Syst. Biol. 52, 229–238 (2003)

    Article  Google Scholar 

  20. Huelsenbeck, J., Bollback, J., Levine, A.: Inferring the root of a phylogenetic tree. Syst. Biol. 51, 32–43 (2002)

    Article  Google Scholar 

  21. McMorris, F.R., Steel, M.A.: The complexity of the median procedure for binary trees. In: Proceedings of the International Federation of Classification Societies (1993)

    Google Scholar 

  22. Pisani, D., Wilkinson, M.: MRP, taxonomic congruence and total evidence. Systematic Biology 51, 151–155 (2002)

    Article  Google Scholar 

  23. Pisani, D., Yates, A.M., Langer, M.C., Benton, M.J.: A genus-level supertree of the Dinosauria. Proceedings of the Royal Society of London 269, 915–921 (2002)

    Article  Google Scholar 

  24. Purvis, A.: A modification to Baum and Ragan’s method for combining phylogenetic trees. Systematic Biology 44, 251–255 (1995)

    Article  Google Scholar 

  25. Ragan, M.A.: Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution 1, 53–58 (1992)

    Article  Google Scholar 

  26. Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Mathematical Biosciences 53, 131–147 (1981)

    Article  MathSciNet  MATH  Google Scholar 

  27. Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)

    MATH  Google Scholar 

  28. Smith, A.: Rooting molecular trees: problems and strategies. Biol. J. Linn. Soc. 51, 279–292 (1994)

    Article  Google Scholar 

  29. Wheeler, W.: Nucleic acid sequence phylogeny and random outgroups. Cladistics 6, 363–368 (1990)

    Article  Google Scholar 

  30. Yap, V., Speed, T.: Rooting a phylogenetic tree with nonreversible substitution models. BMC Evol. Biol. 5, 2 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, Iowa State University, Ames, IA, 50011, USA

    Ruchi Chaudhary & David Fernández-Baca

  2. Department of Biology, University of Florida, Gainesville, FL, 32611, USA

    J. Gordon Burleigh

Authors
  1. Ruchi Chaudhary
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. Gordon Burleigh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David Fernández-Baca
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Chaudhary, R., Burleigh, J.G., Fernández-Baca, D. (2011). Fast Local Search for Unrooted Robinson-Foulds Supertrees. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_20

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-21260-4_20

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

  • Online ISBN: 978-3-642-21260-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation