We address the problem of constructing phylogenetic networks using two criteria: the number of cycles and the fit value of the network. Traditionally the fit value is the main objective for evaluating phylogenetic networks. However, a small number of cycles in a network is desired and pointed out in several publications.

We propose a new phylogenetic network called CS-network and a method for constructing it. The method is based on the well-known splitstree method. A CS-network contains a face which is k-cycle, k ≥ 3 (not as splitstree). We discuss difficulties of using non-parallelogram faces in splitstree networks. Our method involves clustering and optimization of weights of the network edges.

The algorithm for constructing the underlying graph (except the optimization step) has a polynomial time. Experimental results show a good performance of our algorithm.


Short Path Network Construction Phylogenetic Network Network Distance Underlying 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.


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  1. 1.
    Bandelt, H., Dress, A.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92, 47–105 (1992)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Bryant, D., Moulton, V.: Neighbornet: An agglomerative method for the construction of planar phylogenetic networks. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 375–391. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  3. 3.
    Dress, A.: Trees, tight extensions of metric spaces, and the cohomological dimension of certain groups: A note on combinatorial properties of metric spaces. Advances in Mathematics 53, 321–402 (1984)zbMATHCrossRefMathSciNetGoogle Scholar
  4. 4.
    Dress, A., Huson, D.: Constructing splits graphs. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1, 109–115 (2004)CrossRefGoogle Scholar
  5. 5.
    Gusfield, D., Eddhu, S., Langley, C.: The fine structure of galls in phylogenetic networks. INFORMS Journal on Computing 16, 459–469 (2004)CrossRefMathSciNetGoogle Scholar
  6. 6.
    Gusfield, D., Hickerson, D., Eddhu, S.: An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. Discrete Applied Mathematics 155, 806–830 (2007)zbMATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Huson, D.: Splitstree: a program for analyzing and visualizing evolutionary data. Bioinformatics 14, 68–73 (1998)CrossRefGoogle Scholar
  8. 8.
    Huson, D., Bryant, D.: Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267 (2006)CrossRefGoogle Scholar
  9. 9.
    Huson, D., Klöpper, T.: Beyond galled trees - decomposition and computation of galled networks. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 211–225. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  10. 10.
    Koolen, J., Moulton, V., Tönges, U.: A classification of the six-point prime metrics. Europ. J. Combinatorics 21, 815–829 (2000)zbMATHCrossRefGoogle Scholar
  11. 11.
    Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., Timme, R.E.: Phylogenetic networks: Modeling, reconstructibility, and accuracy. IEEE/ACM Trans. Comput. Biology Bioinformatics 155(1), 13–23 (2004)CrossRefGoogle Scholar
  12. 12.
    Myers, S., Griffiths, R.: Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375–394 (2003)Google Scholar
  13. 13.
    Nakhleh, L., Warnow, T., Linder, C.R., John, K.St.: Reconstructing reticulate evolution in species: Theory and practice. Journal of Computational Biology 12(6), 796–811 (2005)CrossRefGoogle Scholar
  14. 14.
    Song, Y.S., Wu, Y., Gusfield, D.: Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Advances in Mathematics 21, 413–422 (2005)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Lichen Bao
    • 1
  • Sergey Bereg
    • 1
  1. 1.Department of Computer Science Erik Jonsson School of Engineering & Computer ScienceThe University of Texas at DallasRichardsonUSA

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