Constructing splits graphs

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 1, Issue 3, 2004, Pages 109-115

  Dress, Andreas W M ^a   Huson, Daniel H ^b  

^a MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Graph drawing; Phylogenetic networks; Splits graphs

Indexed keywords

ALGORITHMS; GENES; MATHEMATICAL MODELS; SET THEORY; THEOREM PROVING; VECTORS; VISUALIZATION;

GRAPH DRAWING; GRAPHICAL REPRESENTATION; PHYLOGENETIC NETWORKS; SPLITS GRAPHS;

GRAPH THEORY;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; SOFTWARE;

EID: 14744273276     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2004.27     Document Type: Article

References (23)

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. H.J. Bandelt, P. Forster, B.C. Sykes, and M.B. Richards, "Mitochondrial Portraits of Human Population Using Median Networks," Genetics, vol. 141, pp. 743-753, Oct. 1995.
3. J. Bohne, A.M.W. Dress, and S. Fischer, "A Simple Proof for de Bruijn's Dualization Principle," Sankhya Ser. A, vol. 54, special issue, combinatorial math. and applications (Calcutta, 1988), pp. 77-84, 1992.
4. S. Booth and S. Luecker, "Testing for the Consecutive Ones Property, Interval Graphs and Graph Planarity Using PQ-Tree Algorithms," J. Computer and System Sciences, vol. 13, pp. 335-379, 1976.
5. D. Bryant, D.H. Huson, T. Kloepper, and K. Nieselt-Struwe, "Distance Corrections on Recombinant Sequences," Proc. Workshop Algorithms in Bioinformatics, 2003.
6. D. Bryant and V. Moulton, "NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks," Algorithms in Bioinformatics, WABI 2002, R. Guigó and D. Gusfield, eds., pp. 375-391, 2002.
7. P. Buneman, "The Recovery of Trees from Measures of Dissimlarity," Math. and the Archeological and Historical Sciences, pp. 387-395, Edinburgh Univ. Press, 1971.
8. N.G. de Brujin, "Dualization of Multigrids," J. Physique, Proc. Int'l Workshop Aperiodic Crystals, vol. 47, no. 7, Suppl. Colloq. C3, pp. C39-C318, 1986.
9. A.W.M. Dress, D.H. Huson, and V. Moulton, "Analyzing and Visualizing Sequence and Distance Data Using Splitstree," Discrete and Applied Math., vol. 71, pp. 95-109, 1996.
10. J. Felsenstein, Inferring Phylogenies. Sinauer Assoc., Inc., 2004.
11. D. Gusfield, S. Eddhu, and C. Langley, "Efficient Reconstruction of Phylgenetic Networks with Constrained Recombination," Proc. 2003 IEEE CSB Bioinformatics Conf., 2003.
12. B. Holland and V. Moulton, "Consensus Networks: A Method for Visualizing Incompatibilities in Collections of Trees," Proc. Workshop Algorithms in Bioinformatics, pp. 165-176, 2003.
13. K.T. Huber, M. Langton, D. Penny, V. Moulton, and M. Hendy, "Spectronet: A Package for Computing Spectra and Median Networks," Applied Bioinformatics, vol. 1, pp. 159-161, 2002.
14. D.H. Huson and D. Bryant, "Estimating Phylogenetic Trees and Networks Using Splitstree 4," manuscript in preparation, software available from www-ab.informatik.uni-tuebingen.de/software, 2004.
15. D.H. Huson, "Splitstree: A Program for Analyzing and Visualizing Evolutionary Data," Bioinformatics, vol. 14, no. 10, pp. 68-73, 1998.
16. D.H. Huson, T. Dezulian, T. Kloepper, and M.A. Steel, "Phylogenetic Super-Networks from Partial Trees," Proc. Workshop Algorithms in Bioinformatics, 2004.
17. P.J. Lockhart, P.A. McLenachan, D. Havell, D. Glenny, D.H. Huson, and U. Jensen, "Phylogeny, Dispersal and Radiation of New Zealand Alpine Buttercups: Molecular Evidence under Split Decomposition," Ann Missouri Bot Gard, vol. 88, pp. 458-477, 2001.
18. L. Nakhleh, T. Warnow, and C.R. Linder, "Reconstructing Reticulate Evolution in Species-Theory and Practice," Proc. RECOMB '04, pp. 337-346, 2004.
19. D. Posada, "Evalutation of Methods for Detecting Recombination from DNA Sequences," Molecular Biology and Evolution, vol. 19, no. 5, pp. 708-717, 2002.
20. D. Posada and K.A. Crandall, "Intraspecific Gene Genealogies: Trees Grafting into Networks," Trends in Ecology ana Evolution, vol. 16, no. 1, pp. 37-45, 2001.
21. N. Saitou and M. Nei, "The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees," Molecular Biology and Evolution, vol. 4, pp. 406-425, 1987.
22. D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, "Chapter 11: Phylogenetic Inference," Molecular Systematics, D.M. Hillis, C. Moritz, and B.K. Mable, eds., pp. 407-514, Sinauer Assoc., Inc., second ed., 1996.
23. R. Wetzel, "Zur Visualisierung Abstrakter, Ahnlichkeitsbeziehungen, " PhD thesis, Univ. of Bielefeld, 1995.