The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.01 - January-March (2009 vol.6)
pp: 103-109
Daniel H. Huson , Tuebinge University, Tuebingen
ABSTRACT
The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation and visualization. In this paper we discuss the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees. Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs.
INDEX TERMS
rooted phylogenetic networks, graph drawing
CITATION
Daniel H. Huson, "Drawing Rooted Phylogenetic Networks", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, no. 1, pp. 103-109, January-March 2009, doi:10.1109/TCBB.2008.58
REFERENCES
[1] H.-J. Bandelt and A.W.M. Dress, “A Canonical Decomposition Theory for Metrics on a Finite Set,” Advances in Math., vol. 92, pp.47-105, 1992.
[2] M. Bordewich, S. Linz, K. St. John, and C. Semple, “A Reduction Algorithm for Computing the Hybridization Number of Two Trees,” Evolutionary Bioinformatics, vol. 3, pp. 86-98, 2007.
[3] M. Bordewich and C. Semple, “Computing the Minimum Number of Hybridization Events for a Consistent Evolutionary History,” Discrete Applied Math., vol. 155, no. 8, pp. 914-928, 2007.
[4] J.E. Cohen, “Mathematics is Biology's Next Microscope, Only Better; Biology is Mathematics' Next Physics, Only Better,” PLoS Biology, vol. 2, no. 12, p. e439, 2004.
[5] W.F. Doolittle and E. Bapteste, “Pattern Pluralism and the Tree of Life Hypothesis,” Proc. Nat'l Academy of Sciences USA, vol. 104, pp. 2043-2049, 2007.
[6] A.W.M. Dress and D.H. Huson, “Constructing Splits Graphs,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 1, no. 3, pp. 109-115, July-Sept. 2004.
[7] J. Felsenstein, Inferring Phylogenies. Sinauer Assoc., Inc., 2004.
[8] P. Gambette and D.H. Huson, “Improved Layout of Phylogenetic Networks,” IEEE/ACM Trans. Computational Biology and Bioinformatics, 2005.
[9] M.R. Garey and D.S. Johnson, “Crossing Number is NP-Complete,” SIAM J. Algebraic Discrete Methods, vol. 4, pp.312-316, 1983.
[10] D. Gusfield and V. Bansal, “A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters,” Proc. Ninth Int'l Conf. Research in Computational Molecular Biology (RECOMB '05), pp. 217-232, 2005.
[11] D. Gusfield, V. Bansal, V. Bafna, and Y.S. Song, “A Decomposition Theory for Phylogenetic Networks and Incompatible Characters,” J. Computational Biology, vol. 14, pp. 1247-1272, 2007.
[12] J. Hein, “Reconstructing Evolution of Sequences Subject to Recombination Using Parsimony,” Math. Biosciences, pp. 185-200, 1990.
[13] D.H. Huson and D. Bryant, “Application of Phylogenetic Networks in Evolutionary Studies,” Molecular Biology and Evolution, vol. 23, pp. 254-267, , 2006.
[14] D.H. Huson, T. Kloepper, P.J. Lockhart, and M.A. Steel, “Reconstruction of Reticulate Networks from Gene Trees,” Proc. Ninth Int'l Conf. Research in Computational Molecular Biology (RECOMB '05), pp. 233-249, 2005.
[15] D.H. Huson and T.H. Kloepper, “Computing Recombination Networks from Binary Sequences,” Bioinformatics, vol. 21, no. Suppl. 2, pp.ii159-ii165, ECCB, 2005.
[16] D.H. Huson, D.C. Richter, C. Rausch, T. Dezulian, M. Franz, and R. Rupp, “Dendroscope: An Interactive Viewer for Large Phylogenetic Trees,” BMC Bioinformatics, vol. 8, www.splitstree.orgwww.dendroscope.org, 2007, 460doi:10.1186/1471-2105-8-460.
[17] D.H. Huson and R. Rupp, “Summarizing Multiple Gene Trees Using Cluster Networks,” submitted to Proc. 16th Ann. Int'l Conf. Intelligent Systems for Molecular Biology (ISMB), 2008.
[18] G. Jin, L. Nakhleh, S. Snir, and T. Tuller, “Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study,” Molecular Biology and Evolution, vol. 24, pp. 324-337, 2006.
[19] T.H. Kloepper and D.H. Huson, “Drawing Explicit Phylogenetic Networks and Their Integration into SplitsTree,” BMC Evolutionary Biology, 2008.
[20] J. Leebens-Mack, L.A. Raubeson, L. Cui, J.V. Kuehl, M.H. Fourcade, T.W. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis, “Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone,” Molecular Biology and Evolution, vol. 22, no. 10, pp. 1948-1963, 2005.
[21] C.R. Linder and L.H. Rieseberg, “Reconstructing Patterns of Reticulate Evolution in Plants,” Am. J. Botany, vol. 91, no. 10, pp.1700-1708, 2004.
[22] L. Nakhleh, T. Warnow, and C.R. Linder, “Reconstructing Reticulate Evolution in Species—Theory and Practice,” Proc. Eighth Int'l Conf. Research in Computational Molecular Biology (RECOMB '04), pp. 337-346, 2004.
[23] C. Semple and M.A. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[24] K. Sugiyama, S. Tagawa, and M. Toda, “Methods for Visual Understanding of Hierarchical System Structures,” IEEE Trans. Systems, Man, and Cybernetics, vol. 11, pp. 109-125, 1981.
16 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool