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Steven M. Kelk, Celine Scornavacca, Leo van Iersel, "On the Elusiveness of Clusters," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 517534, March/April, 2012.  
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@article{ 10.1109/TCBB.2011.128, author = {Steven M. Kelk and Celine Scornavacca and Leo van Iersel}, title = {On the Elusiveness of Clusters}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {2}, issn = {15455963}, year = {2012}, pages = {517534}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.128}, 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  On the Elusiveness of Clusters IS  2 SN  15455963 SP517 EP534 EPD  517534 A1  Steven M. Kelk, A1  Celine Scornavacca, A1  Leo van Iersel, PY  2012 KW  Rooted phylogenetic networks KW  clusters KW  reticulate evolution KW  parsimony KW  computational complexity KW  polynomialtime algorithms. VL  9 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[2] Mathematics of Evolution and Phylogeny, O. Gascuel, ed. Oxford Univ. Press, Inc., http://portal.acm.orgcitation.cfm?id=1557209 , 2005.
[3] Reconstructing Evolution: New Mathematical and Computational Advances, O. Gascuel and M. Steel, eds. Oxford Univ. Press, http://www.amazon.com/exec/obidos/redirect?tag=citeulike0720&path=ASIN 0199208220 , 2007.
[4] D.H. Huson, R. Rupp, and C. Scornavacca, Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge Univ. Press, 2011.
[5] L. Nakhleh, “Evolutionary Phylogenetic Networks: Models and Issues,” The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2009.
[6] C. Semple, “Hybridization Networks,” Reconstructing Evolution  New Mathematical and Computational Advances, Oxford Univ. Press, 2007.
[7] D.H. Huson, R. Rupp, V. Berry, P. Gambette, and C. Paul, “Computing Galled Networks from Real Data,” Bioinformatics, vol. 25, no. 12, pp. i85i93, 2009.
[8] L.J.J. van Iersel and S.M. Kelk, “When Two Trees Go to War,” J. Theoretical Biology, vol. 269, no. 1, pp. 245255, 2011.
[9] J. Jansson and W.K. Sung, “Inferring a Level1 Phylogenetic Network from a Dense Set of Rooted Triplets,” Theoretical Computer Science, vol. 363, no. 1, pp. 6068, 2006.
[10] J. Jansson, N.B. Nguyen, and W.K. Sung, “Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network,” SIAM J. Computing, vol. 35, no. 5, pp. 10981121, 2006.
[11] L.J.J. van Iersel, J.C.M. Keijsper, S.M. Kelk, L. Stougie, F. Hagen, and T. Boekhout, “Constructing Level2 Phylogenetic Networks from Triplets,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 667681, Oct.Dec. 2009.
[12] L.J.J. van Iersel, S.M. Kelk, and M. Mnich, “Uniqueness, Intractability and Exact Algorithms: Reflections on Level$k$ Phylogenetic Networks,” J. Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 597623, 2009.
[13] T.H. To and M. Habib, “Level$k$ Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time,” Proc. Conf. Combinatorial Pattern Matching (CPM '09), pp. 275288, 2009.
[14] 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. 914928, 2007.
[15] M. Bordewich, S. Linz, K.S. John, and C. Semple, “A Reduction Algorithm for Computing the Hybridization Number of Two Trees,” Evolutionary Bioinformatics, vol. 3, pp. 8698, 2007.
[16] M. Bordewich and C. Semple, “Computing the Hybridization Number of Two Phylogenetic Trees Is FixedParameter Tractable,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 4, no. 3, pp. 458466, JulySept. 2007.
[17] J. Collins, S. Linz, and C. Semple, “Quantifying Hybridization in Realistic Time,” J. Computational Biology, vol. 18, no. 10, pp 13051318, 2011.
[18] Y. Wu and W. Jiayin, “Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees,” Proc. Sixth Int'l Symp. Bioinformatics Research and Applications (ISBRA), vol. 6053, pp. 203214, 2010.
[19] Y. Wu, “Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees,” Bioinformatics, vol. 26, pp. i140i148, 2010.
[20] T. Huynh, J. Jansson, N. Nguyen, and W.K. Sung, “Constructing a Smallest Refining Galled Phylogenetic Network,” Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 265280, 2005.
[21] L. van Iersel and S. Kelk, “Constructing the Simplest Possible Phylogenetic Network from Triplets,” Algorithmica, pp. 129, Springer, http://dx.doi.org/10.1007s0045300993330 , 2009.
[22] D. Gusfield, V. Bansal, V. Bafna, and Y. Song, “A Decomposition Theory for Phylogenetic Networks and Incompatible Characters,” J. Computational Biology, vol. 14, no. 10, pp. 12471272, 2007.
[23] D. Gusfield, D. Hickerson, and S. Eddhu, “An Efficiently Computed Lower Bound on the Number of Recombinations in Phylognetic Networks: Theory and Empirical Study,” Discrete Applied Math., vol. 155, nos. 6/7, pp. 806830, 2007.
[24] Y. Wu and D. Gusfield, “A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem,” J. Combinatorial Optimization, vol. 16, no. 3, pp. 229247, 2008.
[25] S.R. Myers and R.C. Griffiths, “Bounds on the Minimum Number of Recombination Events in a Sample History,” Genetics, vol. 163, pp. 375394, 2003.
[26] D.H. Huson and T.H. Klöpper, “Beyond Galled Trees—Decomposition and Computation of Galled Networks,” Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 211225, 2007.
[27] L.J.J. van Iersel, S.M. Kelk, R. Rupp, and D.H. Huson, “Phylogenetic Networks Do Not Need to be Complex: Using Fewer Reticulations to Represent Conflicting Clusters,” Bioinformatics, vol. 26, pp. i124i131, 2010.
[28] D. Huson and C. Scornavacca, “Dendroscope 3—A Program for Computing and Drawing Rooted Phylogenetic Trees and Networks,” in Preparation. Software Available from: www. dendroscope.org, 2011.
[29] S. Linz and C. Semple, “Hybridization in NonBinary Trees,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 3045, Jan.Mar. 2009.
[30] P. Gambette, V. Berry, and C. Paul, “The Structure of Levelk Phylogenetic Networks,” Proc. 20th Ann. Symp. Combinatorial Pattern Matching, pp. 289300, http://dx.doi.org/10.10079783642024412_26 , 2009.
[31] P. Gambette, “Generators  Building Level$k$ Generators,” http://www.lirmm.fr/gambetteProgGenerators.php , 2011.
[32] V. Bafna and V. Bansal, “Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots,” J. Computational Biology, vol. 13, pp. 501521, 2006.