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An Optimal Algorithm for Building the Majority Rule Consensus Tree

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Research in Computational Molecular Biology (RECOMB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7821))

Abstract

A deterministic algorithm for building the majority rule consensus tree of an input collection of conflicting phylogenetic trees with identical leaf labels is presented. Its worst-case running time is O(n k), where n is the size of the leaf label set and k is the number of input phylogenetic trees. This is optimal since the input size is Ω(n k). Experimental results show that the algorithm is fast in practice.

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References

  1. Adams III., E.N.: Consensus techniques and the comparison of taxonomic trees. Systematic Zoology 21(4), 390–397 (1972)

    Article  Google Scholar 

  2. Amenta, N., Clarke, F., St. John, K.: A Linear-Time Majority Tree Algorithm. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 216–227. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  3. Bansal, M.S., Dong, J., Fernández-Baca, D.: Comparing and aggregating partially resolved trees. Theoretical Computer Science 412(48), 6634–6652 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  4. Boyer, R.S., Moore, J.S.: MJRTY – A Fast Majority Vote Algorithm. In: Boyer, R.S. (ed.) Automated Reasoning: Essays in Honor of Woody Bledsoe. Automated Reasoning Series, pp. 105–117. Kluwer Academic Publishers (1991)

    Google Scholar 

  5. Bryant, D.: A classification of consensus methods for phylogenetics. In: Janowitz, M.F., Lapointe, F.-J., McMorris, F.R., Mirkin, B., Roberts, F.S. (eds.) Bioconsensus. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 61, pp. 163–184. American Mathematical Society (2003)

    Google Scholar 

  6. Day, W.H.E.: Optimal algorithms for comparing trees with labeled leaves. Journal of Classification 2(1), 7–28 (1985)

    Article  MathSciNet  MATH  Google Scholar 

  7. Degnan, J.H., DeGiorgio, M., Bryant, D., Rosenberg, N.A.: Properties of consensus methods for inferring species trees from gene trees. Systematic Biology 58(1), 35–54 (2009)

    Article  Google Scholar 

  8. Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc., Sunderland (2004)

    Google Scholar 

  9. Felsenstein, J.: PHYLIP, version 3.6. Software package, Department of Genome Sciences, University of Washington, Seattle, U.S.A. (2005)

    Google Scholar 

  10. Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, New York (1997)

    Book  MATH  Google Scholar 

  11. Jansson, J., Shen, C., Sung, W.-K.: Improved algorithms for constructing consensus trees. In: Proceedings of the 24th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2013, pp. 1800–1813. SIAM (2013)

    Google Scholar 

  12. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11(3), 459–468 (1994)

    Google Scholar 

  13. Margush, T., McMorris, F.R.: Consensus n-Trees. Bulletin of Mathematical Biology 43(2), 239–244 (1981)

    MathSciNet  MATH  Google Scholar 

  14. Nakhleh, L., Warnow, T., Ringe, D., Evans, S.N.: A comparison of phylogenetic reconstruction methods on an Indo-European dataset. Transactions of the Philological Society 103(2), 171–192 (2005)

    Article  Google Scholar 

  15. Page, R.: COMPONENT, version 2.0. Software package. University of Glasgow, U.K. (1993)

    Google Scholar 

  16. Ronquist, F., Huelsenbeck, J.P.: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12), 1572–1574 (2003)

    Article  Google Scholar 

  17. Semple, C., Steel, M.: Phylogenetics. Oxford Lecture Series in Mathematics and its Applications, vol. 24. Oxford University Press (2003)

    Google Scholar 

  18. Sukumaran, J., Holder, M.T.: DendroPy: a Python library for phylogenetic computing. Bioinformatics 26(12), 1569–1571 (2010)

    Article  Google Scholar 

  19. Sung, W.-K.: Algorithms in Bioinformatics: A Practical Introduction. Chapman & Hall/CRC (2010)

    Google Scholar 

  20. Swofford, D.L.: PAUP*, version 4.0. Software package. Sinauer Associates, Inc., Sunderland (2003)

    Google Scholar 

  21. Wareham, H.T.: An efficient algorithm for computing M l consensus trees. B.Sc. Honours thesis, Memorial University of Newfoundland, Canada (1985)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory of Mathematical Bioinformatics (Akutsu Laboratory), Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan

    Jesper Jansson

  2. Stanford University, 450 Serra Mall, Stanford, CA, 94305-2004, U.S.A.

    Chuanqi Shen

  3. School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417

    Wing-Kin Sung

  4. Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore, 138672

    Wing-Kin Sung

Authors
  1. Jesper Jansson
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  2. Chuanqi Shen
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  3. Wing-Kin Sung
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Editor information

Editors and Affiliations

  1. School of Mathematics, Peking University, Beijing, P.R. China

    Minghua Deng

  2. Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, 100084, Beijing, P.R. China

    Rui Jiang

  3. Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA

    Fengzhu Sun

  4. Department of Automation, Tsinghua University, P.O. Box, 100084, Beijing, China

    Xuegong Zhang

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Jansson, J., Shen, C., Sung, WK. (2013). An Optimal Algorithm for Building the Majority Rule Consensus Tree. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_8

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  • DOI: https://doi.org/10.1007/978-3-642-37195-0_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37194-3

  • Online ISBN: 978-3-642-37195-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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