The Community for Technology Leaders
RSS Icon
Issue No.02 - March/April (2012 vol.9)
pp: 395-407
A. Spillner , Dept. of Math. & Comput. Sci., Univ. of Greifswald, Greifswald, Germany
B. T. Nguyen , Sch. of Comput. Sci., Univ. of East Anglia, Norwich, UK
V. Moulton , Sch. of Comput. Sci., Univ. of East Anglia, Norwich, UK
Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be generated using the SplitsTree package. Recently, the NeighborNet method for generating split networks has become rather popular, in part because it is guaranteed to always generate a circular split system, which can always be displayed by a planar split network. Even so, labels must be placed on the "outside” of the network, which might be problematic in some applications. To help circumvent this problem, it can be helpful to consider so-called flat split systems, which can be displayed by planar split networks where labels are allowed on the inside of the network too. Here, we present a new algorithm that is guaranteed to compute a minimal planar split network displaying a flat split system in polynomial time, provided the split system is given in a certain format. We will also briefly discuss two heuristics that could be useful for analyzing phylogeographic data and that allow the computation of flat split systems in this format in polynomial time.
Phylogeny, Polynomials, Bioinformatics, Computational biology, Image color analysis, Electronic mail, Euclidean distance,flat split system., Phylogenetic tree, split, planar split network, regular split network
A. Spillner, B. T. Nguyen, V. Moulton, "Constructing and Drawing Regular Planar Split Networks", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 2, pp. 395-407, March/April 2012, doi:10.1109/TCBB.2011.115
[1] H.-J. Bandelt and A. Dress, “Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data,” Molecular Phylogenetics and Evolution, vol. 1, pp. 242-252, 1992.
[2] D. Huson and D. Bryant, “Application of Phylogenetic Networks in Evolutionary Studies,” Molecular Biology and Evolution, vol. 23, pp. 254-267, 2006.
[3] D. Bryant and V. Moulton, “NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks,” Molecular Biology and Evolution, vol. 21, pp. 255-265, 2004.
[4] A. Dress and D. Huson, “Constructing Split Graphs,” IEEE Trans. Computational Biology and Bioinformatics, vol. 1, no. 3, pp. 109-115, July 2004.
[5] J. Stavrinides and D. Guttman, “Mosaic Evolution of the Severe Acute Respiratory Syndrome Coronavirus,” J. Virology, vol. 78, pp. 76-82, 2004.
[6] D. Bryant and A. Dress, “Linearly Independent Split Systems,” European J. Combinatorics, vol. 28, pp. 1814-1831, 2007.
[7] P. Gambette and D. Huson, “Improved Layout of Phylogenetic Networks,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 5, no. 3, pp. 472-479, July-Sept. 2008.
[8] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[9] G. Stone, R. Atkinson, A. Rokas, G. Csóka, and J. Nieves-Aldrey, “Differential Success in Northwards Range Expansion Between Ecotypes of the Marble Gallwasp Andricus kollari: A Tale of Two Lifecycles,” Molecular Ecology, vol. 10, pp. 761-778, 2001.
[10] G. Stone, R. Challis, R. Atkinson, G. Csóka, A. Hayward, G. Melika, S. Mutun, S. Preuss, A. Rokas, E. Sadeghi, and K. Schönrogge, “The Phylogeographical Clade Trade: Tracing the Impact of Human-Mediated Dispersal on the Colonization of Northern Europe by the Oak Gallwasp Andricus kollari,” Molecular Ecology, vol. 16, pp. 2768-2781, 2007.
[11] S. Felsner, Geometric Graphs and Arrangements. Vieweg, 2004.
[12] H.-J. Bandelt and A. Dress, “A Canonical Decomposition Theory for Metrics on a Finite Set,” Advances in Math., vol. 92, pp. 47-105, 1992.
[13] G. Ringel, “Teilungen der Ebene Durch Geraden Und Topologische Geraden,” Mathematische Zeitschrift, vol. 64, pp. 79-102, 1956.
[14] A. Björner, M. Las Vergnas, N. White, B. Sturmfels, and G. Ziegler, Oriented Matroids. Cambridge Univ. Press, 1993.
[15] L. Bao and S. Bereg, “Counting Faces in Split Networks,” Proc. Int'l Symp. Bioinformatics Research and Applications, pp. 112-123, 2009.
[16] J. Bondy and U. Murty, Graph Theory. Springer, 2008.
[17] P. Agarwal and M. Sharir, “Pseudo-Line Arrangements: Duality, Algorithms, and Applications,” SIAM J. Computing, vol. 34, pp. 526-552, 2005.
[18] F. Tschirschnitz, “Testing Extendability for Partial Chirotopes Is NP-Complete,” Proc. Canadian Conf. Computational Geometry (CCCG), pp. 165-168, 2001.
[19] H. Prasanna and M. Rai, “Detection and Frequency of Recombination in Tomato-Infecting Begomoviruses of South and Southeast Asia,” Virology J., vol. 4, article 111, 2007.
[20] S. Grünewald, K. Forslund, A. Dress, and V. Moulton, “QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets,” Molecular Biology and Evolution, vol. 24, pp. 532-538, 2007.
[21] J. Kruskal and M. Wish, Multidimensional Scaling. Sage Publications, 1978.
[22] J. Triplett, K. Oltrogge, and L. Clark, “Phylogenetic Relationships and Natural Hybridization among the North American Woody Bamboos (Poaceae: Bambusoideae: Arundinaria),” Am. J. Botany, vol. 97, pp. 471-492, 2010.
[23], 2011.
45 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool