Abstract
Consider two phylogenetic networks N and N′ of size n. The tripartition-based distance finds the proportion of tripartitions which are not shared by N and N′. This distance is proposed by Moret et al (2004) and is a generalization of Robinson-Foulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min{kn log n, n log n + hn})-time algorithm to compute this distance, where h is the number of hybrid nodes in N and N′ while k is the maximum number of hybrid nodes among all biconnected components in N and N′. Note that k << h << n in a phylogenetic network. In addition, we propose algorithms for comparing galled-trees, which are an important, biological meaningful special case of phylogenetic network. We give an O(n)-time algorithm for comparing two galled-trees. We also give an O(n + kh)-time algorithm for comparing a galled-tree with another general network, where h and k are the number of hybrid nodes in the latter network and its biggest biconnected component respectively.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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)
Choy, C., Jansson, J., Sadakane, K., Sung, W.-K.: Computing the maximum agreement of phylogenetic networks. Theoretical Computer Science 335(1), 93–107 (2005)
Doolittle, W.F.: Phylogenetic classification and the universal tree. Science 284, 2124–2128 (1999)
Gusfield, D., Bansal, V.: A fundamental decomposition theory for phylogenetic networks and incompatible characters. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 217–232. Springer, Heidelberg (2005)
Gusfield, D., Eddhu, S., Langley, C.: Efficient reconstruction of phylogenetic networks with constrained recombination. In: Proc. of the Computational Systems Bioinformatics Conference (CSB 2003), pp. 363–374 (2003)
Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Mathematical Biosciences 98(2), 185–200 (1990)
Hon, W.-K., Kao, M.-Y., Lam, T.W., Sung, W.-K., Yiu, S.-M.: Non-shared edges and nearest neighbor interchanges revisited. Inf. Process. Lett. 91(3), 129–134 (2004)
Huson, D.H., Dezulian, T., Klöpper, T., Steel, M.: Phylogenetic super-networks from partial trees. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 388–399. Springer, Heidelberg (2004)
Huson, D.H., Klopper, T., Lockhart, P.J., Steel, M.A.: Reconstruction of reticulate networks from gene trees. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 233–249. Springer, Heidelberg (2005)
Huynh, T.N.D., Jansson, J., Nguyen, N.B., Sung, W.K.: Constructing a smallest refining galled phylogenetic network. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 265–280. Springer, Heidelberg (2005)
Jansson, J., Nguyen, N.B., Sung, W.K.: Algorithms for combining rooted triplets into a galled phylogenetic network. In: Proc. of the 16th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2005), pp. 349–358 (2005)
Jansson, J., Sung, W.-K.: Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In: Chwa, K.-Y., Munro, J.I.J. (eds.) COCOON 2004. LNCS, vol. 3106, pp. 462–471. Springer, Heidelberg (2004)
Jansson, J., Sung, W.K.: The maximum agreement of two nested phylogenetic networks. In: Fleischer, R., Trippen, G. (eds.) ISAAC 2004. LNCS, vol. 3341, pp. 581–593. Springer, Heidelberg (2004)
Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., Timme, R.: Phylogenetic networks: Modeling, reconstructibility, and accuracy. IEEE Transactions on Computational Biology and Bioinformatics 1(1), 1–12 (2004)
Nakhleh, L., Sun, J., Warnow, T., Linder, C.R., Moret, B.M.E., Tholse, A.: Towards the development of computational tools for evaluating phylogenetic reconstruction methods. In: Proc. of the 8th Pacific Symposium on Biocomputing (PSB 2003), pp. 315–326 (2003)
Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species – theory and practice. In: Proc. of the 8th Annual International Conf. on Research in Computational Molecular Biology (RECOMB 2004), pp. 337–346 (2004)
Posada, D., Crandall, K.A.: Intraspecific gene genealogies: trees grafting into networks. TRENDS in Ecology & Evolution 16(1), 37–45 (2001)
Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Mathematical Biosciences 53, 131–147 (1981)
Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8(1), 69–78 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Nguyen, N.B., Nguyen, C.T., Sung, WK. (2005). Fast Algorithms for Computing the Tripartition-Based Distance Between Phylogenetic Networks. In: Deng, X., Du, DZ. (eds) Algorithms and Computation. ISAAC 2005. Lecture Notes in Computer Science, vol 3827. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11602613_41
Download citation
DOI: https://doi.org/10.1007/11602613_41
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-30935-2
Online ISBN: 978-3-540-32426-3
eBook Packages: Computer ScienceComputer Science (R0)