Parallel Construction of Conflict Graph for Phylogenetic Network Problem

  • D. S. Rao
  • G. N. Kumar
  • Dheeresh K. Mallick
  • Prasanta K. Jana
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4815)


Conflict graph is used as the major tool in various algorithms [14] - [18] for solving the phylogenetic network problem. The over all time complexity of these algorithms mainly depends on the construction of the conflict graph. In this paper, we present a parallel algorithm for building a conflict graph. Given a set of n binary sequences, each of size m, our algorithm is mapped on a triangular array in O(n) time using O(m 2) processors.


Parallel Algorithm Binary Sequence Phylogenetic Network Triangular Array Conflict Graph 
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.


  1. 1.
    Gusfield, D.: Efficient algorithms for inferring evolutionary trees. Networks 21, 19–28 (1991)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Schierup, M.H., Hein, J.: Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879–891 (2000)Google Scholar
  3. 3.
    Schierup, M.H., Hein, J.: Recombination and the molecular clock. Mol. Biol. Evol. 17, 1578–1579 (2000)Google Scholar
  4. 4.
    Posada, D., Crandall, K.: The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution 54, 396–402 (2002)Google Scholar
  5. 5.
    Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98, 185–200 (1990)zbMATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Hein, J.: A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36, 396–405 (1993)CrossRefGoogle Scholar
  7. 7.
    Song, Y., Hein, J.: On the minimum number of recombination events in the evolutionary history of DNA sequences. Journal of Mathematical Biology 48, 160–186 (2003)CrossRefMathSciNetGoogle Scholar
  8. 8.
    Song, Y., Hein, J.: Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In: Proc. of 2003 Workshop on Algorithms in Bioinformatics, Berlin, Germany (2003)Google Scholar
  9. 9.
    Linder, C.R., Moret, B.M.E., Nakhleh, L., Warnow, T.: Reconstructing networks part II: computational aspects. In: the ninth pacific symposium on Biocomputing (2004) Google Scholar
  10. 10.
    Zahid, M.A.H., Mittal, A., Joshi, R.C.: Use of phylogenetic networks and its reconstruction algorithms. Journal of Bioinformatics India 4, 47–58 (2005)Google Scholar
  11. 11.
    Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8, 69–78 (2001)CrossRefGoogle Scholar
  12. 12.
    Hudson, R.R., Kaplan, N.L.: Statistical properties of the number of recombination events in the History of a sample of DNA sequences. Genetics 111, 147–164 (1985)Google Scholar
  13. 13.
    Myers, S.R., Griffths, R.C.: Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375–394 (2003)Google Scholar
  14. 14.
    Gusfield, D., Satish, E., Langley, C.: Efficient reconstruction of phylogenetic networks (of SNPs) with constrained recombination. In: Proceedings of 2nd CSB Bioinformatics Conference, Los Alamitos, CA (2003)Google Scholar
  15. 15.
    Gusfield, D., Satish, E., Langley, C.: Optimal efficient reconstruction of phylogenetic networks with constrained recombination. Journal of Bioinformatics and Computational Biology 2, 173–213 (2004)CrossRefGoogle Scholar
  16. 16.
    Gusfield, D.: Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination, Technical Report, Department of Computer Sc., University of California, Davis, CA Google Scholar
  17. 17.
    Gusfield, D., Satish, E., Langley, C.: The fine structure of galls in phylogenetic networks. Informs Journal on Computing 16, 459–469 (2004)CrossRefMathSciNetGoogle Scholar
  18. 18.
    Bafna, V., Bansal, V.: The number of recombination events in a sample history conflict graph and lower bounds. IEEE Ttrans. on Computational Biology and Bioinformatics 1, 78–90 (2004)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • D. S. Rao
    • 1
  • G. N. Kumar
    • 1
  • Dheeresh K. Mallick
    • 2
  • Prasanta K. Jana
    • 1
  1. 1.Department of Computer Science and Engineering, Indian School of Mines University, Dhanbad - 826 004India
  2. 2.Department of Computer Science and Engineering, Birla Institute of Technology, Mesra, Ranchi – 835 215India

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