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Duhong Chen, Oliver Eulenstein, David Fern?ndezBaca, Michael Sanderson, "MinimumFlip Supertrees: Complexity and Algorithms," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 165173, AprilJune, 2006.  
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@article{ 10.1109/TCBB.2006.26, author = {Duhong Chen and Oliver Eulenstein and David Fern?ndezBaca and Michael Sanderson}, title = {MinimumFlip Supertrees: Complexity and Algorithms}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {3}, number = {2}, issn = {15455963}, year = {2006}, pages = {165173}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2006.26}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  MinimumFlip Supertrees: Complexity and Algorithms IS  2 SN  15455963 SP165 EP173 EPD  165173 A1  Duhong Chen, A1  Oliver Eulenstein, A1  David Fern?ndezBaca, A1  Michael Sanderson, PY  2006 KW  Phylogenetic tree KW  supertree KW  tree assembly KW  NPcompleteness. VL  3 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] D.H. Huson, S.M. Nettles, and T.J. Warnow, “DiskCovering, a FastConverging Method for Phylogenetic Tree Reconstruction,” J. Computational Biology, vol. 6, nos. 34, pp. 369386, 1999.
[2] Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, O.R.P. BinindaEmonds, ed. Kluwer Academic, 2004.
[3] A.D. Gordon, “Consensus Supertrees: The Synthesis of Rooted Trees Containing Overlapping Sets of Labelled Leaves,” J. Classification, vol. 9, pp. 335348, 1986.
[4] M.A. Steel, “The Complexity of Reconstructing Trees from Qualitative Characters and Subtrees,” J. Classification, vol. 9, pp. 91116, 1992.
[5] M.J. Sanderson, A. Purvis, and C. Henze, “Phylogenetic Supertrees: Assembling the Trees of Life,” Trends Ecological Evolution, vol. 13, pp. 105109, 1998.
[6] C. Semple and M.A. Steel, “A Supertree Method for Rooted Trees,” Discrete Applied Math., vol. 105, pp. 147158, 2000.
[7] M.A. Steel, A.W.M. Dress, and S. Böcker, “Simple but Fundamental Limitations on Supertree and Consensus Tree Methods,” Systematic Biology, vol. 49, pp. 363368, 2000.
[8] M.J. Donoghue, “Phylogenies and the Analysis of Evolutionary Sequences, with Examples from Seed Plants,” Evolution, vol. 43, pp. 11371156, 1989.
[9] A. Ortolani, “Spots, Stripes, Tail Tips and Dark Eyes: Predicting the Function of Carnivore Colour Patterns Using the Comparative Method,” Biological J. Linnean Soc., vol. 67, pp. 433476, 1999.
[10] A. Purvis, “A Modification to Baum and Ragan's Method for Combining Phylogenetic Trees,” Systematic Biology, vol. 44, pp. 251255, 1995.
[11] O.R.P. BinindaEmonds, J.L. Gittleman, and A. Purvis, “Building Large Trees by Combining Phylogenetic Information: A Complete Phylogeny of the Extant Carnivora (Mammalia),” Biological Rev., vol. 74, pp. 143175, 1999.
[12] M.F. Wojciechowski, M.J. Sanderson, K.P. Steele, and A. Liston, “Molecular Phylogeny of the `Temperate Herbaceous Tribes' of Papilionoid Legumes: A Supertree Approach,” Advances in Legume Systematics, P. Herendeen and A. Bruneau, eds., vol. 9, pp. 277298, 2000.
[13] F.G.R. Liu, M.M. Miyamoto, N.P. Freire, P.Q. Ong, M.R. Tennant, T.S. Young, and K.F. Gugel, “Molecular and Morphological Supertrees for Eutherian (Placental) Mammals,” Science, vol. 291, pp. 17861789, 2001.
[14] T.J. Davies, T.G. Barraclough, M.W. Chase, P.S. Soltis, D.E. Soltis, and V. Savolainen, “Darwin's Abominable Mystery: Insights from a Supertree of the Angiosperms,” Proc. Nat'l Academy Sciences USA, vol. 101, pp. 19041909, 2004.
[15] E. Grotkopp, M. Rejmanek, M.J. Sanderson, and T.L. Rost, “Evolution of Genome Size in Pines (Pinus) and Its LifeHistory Correlates: Supertree Analyses,” Evolution, pp. 17051729, 2004.
[16] D.R. Brooks, “Hennig's Parasitological Method: A Proposed Solution,” Systems Zoology, vol. 30, pp. 325331, 1981.
[17] B.R. Baum, “Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees,” Taxon, vol. 41, pp. 310, 1992.
[18] M.A. Ragan, “Phylogenetic Inference Based on Matrix Representation of Trees,” Molecular Phylogenetics and Evolution, vol. 1, pp. 5358, 1992.
[19] O. Eulenstein, D. Chen, J.G. Burleigh, D. FernándezBaca, and M.J. Sanderson, “Performance of Flip Supertree Construction with a Heuristic Algorithm,” Systematic Biology, vol. 53, pp. 299308, 2003.
[20] S. Kannan, T. Warnow, and S. Yooseph, “Computing the Local Consensus of Trees,” Proc. Symp. Discrete Algorithms, pp. 6877, 1995.
[21] P. Kearney, M. Li, J. Tsang, and T. Jiang, “Recovering Branches on the Tree of Life: An Approximation Algorithm,” Proc. Symp. Discrete Algorithms, pp. 537546, 1999.
[22] D. Bryant, J. Tsang, P.E. Kearney, and M. Li, “Computing the Quartet Distance between Evolutionary Trees,” Proc. Symp. Discrete Algorithms, pp. 285286, 2000.
[23] A.V. Aho, Y. Sagiv, T.G. Szymanski, and J.D. Ullman, “Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions,” SIAM J. Computing, vol. 10, no. 3, pp. 405421, 1981.
[24] M.R. Henzinger, V. King, and T. Warnow, “Constructing a Tree From Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology,” Algorithmica, vol. 24, pp. 113, 1999.
[25] R.D.M. Page, “Modified Mincut Supertrees,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), D. Gusfield and R. Guigó, eds., pp. 300315, Sept. 2002.
[26] R.L. Graham and L.R. Foulds, “Unlikelihood that Minimal Phylogenies for a Realistic Biological Study Can Be Constructed in Reasonable Computation Time,” Math. Bioscience, vol. 60, pp. 133142, 1982.
[27] J. Felsenstein, “PHYLIP,” http://evolution.genetics.washington. edu phylip.html, 2006.
[28] I. Pe'er, R. Shamir, and R. Sharan, “Incomplete Directed Perfect Phylogeny,” Combinatorial Pattern Matching, R. Giancarlo and D. Sankoff, eds., SpringerVerlag, pp. 143153, 2000.
[29] G.F. Estabrook, C. Johnson, and F.R. McMorris, “An Idealized Concept of the True Cladistic Character?” Math. Bioscience, vol. 23, pp. 263272, 1975.
[30] D. Gusfield, Algorithms on Strings, Trees, and Sequences. New York: Cambridge Univ. Press, 1997.
[31] J.S. Farris, “On Comparing the Shapes of Taxonomic Trees,” Systematic Zoology, vol. 22, pp. 5054, 1976.
[32] D.L. Swofford, G.J. Olsen, P.J. Waddel, and D.M Hillis, “Phylogenetic Inference,” Molecular Systematics, D.M. Hillis, C. Moritz, and B.K. Mable, eds., pp. 407509. Sunderland, Mass.: Sinauer Assoc., 1996.
[33] M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NPCompleteness. New York: W.H. Freeman, 1979.
[34] M. Yannakakis, “Computing the Minimum FillIn Is NPComplete,” SIAM J. Algebraic and Discrete Methods, vol. 2, no. 1, pp. 7779, 1981.
[35] M. Yannakakis, “NodeDeletion Problems on Bipartite Graphs,” SIAM J. Computing, vol. 10, pp. 310326, 1981.
[36] A. Natanzon, R. Shamir, and R. Sharan, “Complexity Classification of Some Edge Modification Problems,” Discrete Applied Math., vol. 113, no. 1, pp. 109128, 2001.
[37] R.G. Downey and M.R. Fellows, Parameterized Complexity. Springer, 1997.
[38] L. Cai, “FixedParameter Tractability of Graph Modification Problems for Hereditary Properties,” Information Processing Letters, vol. 58, pp. 171176, 1996.
[39] D. Gusfield, “Efficient Algorithms for Inferring Evolutionary History,” Networks, vol. 21, pp. 1928, 1992.
[40] J.G. Burleigh, D. Chen, O. Eulenstein, D. FernándezBaca, and M.J. Sanderson, “Minimum Flip Supertrees,” Phylogenetic Supertrees: The Book, Kluwer, to appear.
[41] D. Chen, L. Diao, O. Eulenstein, D. FernándezBaca, and M.J. Sanderson, “Flipping: A Supertree Construction Method,” Bioconsensus, DIMACS: Series in Discrete Math. and Theoretic Computer Science, vol. 61, pp. 135160, Providence, R.I.: Am. Math. Soc., 2003.
[42] D. Chen, O. Eulenstein, and D. FernándezBaca, “Rainbow: A Toolbox for Phylogenetic Supertree Construction and Analysis,” Bioinformatics Advance Access, 2004.