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Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield, "Untangling Tanglegrams: Comparing Trees by Their Drawings," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 4, pp. 588597, OctoberDecember, 2010.  
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@article{ 10.1109/TCBB.2010.57, author = {Balaji Venkatachalam and Jim Apple and Katherine St. John and Dan Gusfield}, title = {Untangling Tanglegrams: Comparing Trees by Their Drawings}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {7}, number = {4}, issn = {15455963}, year = {2010}, pages = {588597}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.57}, 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  Untangling Tanglegrams: Comparing Trees by Their Drawings IS  4 SN  15455963 SP588 EP597 EPD  588597 A1  Balaji Venkatachalam, A1  Jim Apple, A1  Katherine St. John, A1  Dan Gusfield, PY  2010 KW  Optimization KW  combinatorial algorithms KW  graph algorithms KW  trees KW  analysis of algorithms KW  phylogeny KW  tree comparison KW  graph drawing KW  combinatorics. VL  7 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] M.S. Bansal, W.C. Chang, O. Eulenstein, and D. FernándezBaca, "Generalized Binary Tanglegrams: Algorithms and Applications," Proc. First Int'l Conf. Bioinformatics and Computational Biology (BICoB), pp. 114125, 2009.
[2] P. Bertolazzi, G.D. Battista, C. Mannino, and R. Tamassia, "Optimal Upward Planarity Testing of SingleSource Digraphs," SIAM J. Computing, vol. 27, no. 1, pp. 132169, 1998.
[3] D. Bertsimas and R. Weismantel, Optimization Over Integers. Dynamic Ideas, May 2005.
[4] T.C. Biedl, F.J. Brandenburg, and X. Deng, "Crossings and Permutations," Proc. 13th Int'l Symp. Graph Drawing, pp. 112, 2005.
[5] S. Böcker, F. Hffner, A. Truss, and M. Wahlström, "A Faster FixedParameter Approach to Drawing Binary Tanglegrams," Proc. Fourth Int'l Workshop Parameterized and Exact Computation (IWPEC '09), 2009.
[6] M.R. Brown and R.E. Tarjan, "Design and Analysis of a Data Structure for Representing Sorted Lists," SIAM J. Computing, vol. 9, no. 3, pp. 594614, 1980.
[7] K. Buchin, M. Buchin, J. Byrka, M. Nöllenburg, Y. Okamoto, R.I. Silveira, and A. Wolff, "Drawing (Complete) Binary Tanglegrams: Hardness, Approximation, FixedParameter Tractability," Proc. 16th Int'l Symp. Graph Drawing, pp. 324335, 2008.
[8] A. Burt and R. Trivers, Genes in Conflict. Belknap Press of Harvard Univ. Press, 2006.
[9] M. Charleston and S. Perkins, "Lizards, Malaria, and Jungles in the Caribbean," Tangled Trees: Phylogeny, Cospeciation, and Coevolution, R. Page, ed., pp. 6592, Univ. of Chicago Press, 2003.
[10] P. Diaconis and R.L. Graham, "Spearman's Footrule as a Measure of Disarray," J. Royal Statistical Soc. Series B (Methodological), vol. 39, no. 2, pp. 262268, 1977.
[11] R. Diestel, Graph Theory, third ed., SpringerVerlag, 2005.
[12] C. Dwork, R. Kumar, M. Naor, and D. Sivakumar, "Rank Aggregation Methods for the Web," Proc. 10th Int'l Conf. World Wide Web (WWW), pp. 613622, 2001.
[13] T. Dwyer and F. Schreiber, "Optimal Leaf Ordering for Two and a Half Dimensional Phylogenetic Tree Visualisation," Proc. Australasian Symp. Information Visualisation, pp. 109115, 2004.
[14] R. Fagin, R. Kumar, and D. Sivakumar, "Comparing Top k Lists," Proc. 14th Ann. ACMSIAM Symp. Discrete Algorithms (SODA), pp. 2836, 2003.
[15] H. Fernau, M. Kaufmann, and M. Poths, "Comparing Trees via Crossing Minimization," Proc. Ann. Conf. Foundations of Software Technology and Theoretical Computer Science (FSTTCS), pp. 457469, 2005.
[16] L.R. Foulds and R.L. Graham, "The Steiner Problem in Phylogeny is NPComplete," Advances in Applied Math., vol. 3, no. 1, pp. 4349, 1982.
[17] M.R. Garey and D.S. Johnson, "Crossing Number is NPComplete," SIAM J. Algebraic and Discrete Methods, vol. 4, no. 3, pp. 312316, 1983.
[18] D.M. Hillis, T.A. Heath, and K.St. John, "Analysis and Visualization of Tree Space," Systematic Biology, vol. 54, no. 3, pp. 471482, 2005.
[19] R. Hinze and R. Paterson, "Finger Trees: A Simple GeneralPurpose Data Structure," J. Functional Programming, vol. 16, no. 2, pp. 197217, 2006.
[20] D. Holten and J.J. van Wijk, "Visual Comparison of Hierarchically Organized Data," Computer Graphics Forum, vol. 27, no. 3, pp. 759766, 2008.
[21] J.E. Hopcroft and R.E. Tarjan, "Efficient Planarity Testing," J. ACM, vol. 21, no. 4, pp. 549568, 1974.
[22] J.P. Huelsenbeck and F. Ronquist, Mrbayes: Bayesian Inference of Phylogeny, 2001.
[23] H. Kaplan and R.E. Tarjan, "Purely Functional Representations of Catenable Sorted Lists," Proc. 28th Ann. ACM Symp. Theory of Computing (STOC), pp. 202211, 1996.
[24] K. Kawarabayashi and B. Reed, "Computing Crossing Number in Linear Time," Proc. 39th Ann. ACM Symp. Theory of Computing (STOC), pp. 382390, 2007.
[25] J. Lee, "AllDifferent Polytopes," J. Combinatorial Optimization, vol. 6, no. 3, pp. 335352, 2002.
[26] A. Lozano, R.Y. Pinter, O. Rokhlenko, G. Valiente, and M. ZivUkelson, "Seeded Tree Alignment and Planar Tanglegram Layout," Proc. Seventh Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 98110, 2007.
[27] M. Nöllenburg, D. Holten, M. Völker, and A. Wolff, "Drawing Binary Tanglegrams: An Experimental Evaluation," Proc. 11th Workshop Algorithm Eng. and Experiments (ALENEX), pp. 106119, 2009.
[28] R.D.E. Page, Tangled Trees: Phylogeny, Cospeciation, and Coevolution. Univ. of Chicago Press, 2002.
[29] S. Roch, "A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 1, pp. 9294, Jan.Mar. 2006.
[30] W.K. Shih and W.L. Hsu, "A New Planarity Test," Theoretical Computer Science, vol. 223, nos. 12, pp. 179191, 1999.
[31] D.L. Swofford, PAUP∗. Phylogenetic Analysis Using Parsimony (∗and Other Methods), Version 4. Sinauer Assoc., 2002.
[32] D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, "Phylogenetic Inference," Molecular Systematics, second ed., pp. 407514, Sinauer Assoc., 1996.
[33] B. Venkatachalam, J. Apple, K.St. John, and D. Gusfield, "Untangling Tanglegrams: Comparing Trees by Their Drawings," Technical Report CSE20091, UC Davis, Computer Science Dept., 2009.
[34] B. Venkatachalam, J. Apple, K.St. John, and D. Gusfield, "Untangling Tanglegrams: Comparing Trees by Their Drawings," Proc. Fifth Int'l Symp. Bioinformatics Research and Applications (ISBRA '09), pp. 8899, 2009.
[35] W.N. Wan Zainon and P. Calder, "Visualising Phylogenetic Trees," Proc. Seventh Australasian User Interface Conf. (AUIC '06), Conf. Research and Practice in Information Technology (CRPIT), vol. 50, W. Piekarski, ed., pp. 145152, 2006.