Search results for ' JBCB ' :
    30 matches found.
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

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Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.  
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
       
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Matthieu Willems, Nadia Tahiri and Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. In JBCB, Vol. 12(5), 2014.  
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
       
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Celine Scornavacca, Paprotny Wojciech, Vincent Berry and Vincent Ranwez. Representing a set of reconciliations in a compact way. In JBCB, Vol. 11(2):1250025, 2013.  
Keywords: duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801.
       
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Philippe Gambette, Vincent Berry and Christophe Paul. Quartets and Unrooted Phylogenetic Networks. In JBCB, Vol. 10(4):1250004, 2012.  
Keywords: abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network.
Note: http://hal.archives-ouvertes.fr/hal-00678046/en/.
       
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An-Chiang Chu, Jesper Jansson, Richard Lemence, Alban Mancheron and Kun-Mao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177-188 of LNCS, springer, 2012.  
Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network.
Note: preliminary version.
       
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Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385-398 of LNCS, springer, 2012.  
Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.
       
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Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012.  
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
       
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Michel Habib and Thu-Hien To. Constructing a Minimum Phylogenetic Network from a Dense Triplet Set. In JBCB, Vol. 10(5):1250013, 2012.  
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1103.2266.
       
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Ruogu Sheng and Sergey Bereg. Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks. In JBCB, Vol. 10(6):1250017, 2012.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction.
       
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Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011.  
Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.
       
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Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010.  
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
       
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Leo van Iersel, Steven Kelk and Matthias Mnich. Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks. In JBCB, Vol. 7(4):597-623, 2009.  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/pdf/0712.2932v2.
       

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Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.  
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.
       
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Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In Oleg N. Terikhovsky and William N. Burton editors, New Topics in Theoretical Computer Science, Pages 119-141, Nova Publishers, 2008.  
Keywords: dynamic programming, MASN, nested network, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested12_NTTCS2008_corrected.pdf.
       

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Yufeng Wu and Dan Gusfield. Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) In JBCB, Vol. 5(2(a)):181-200, 2007.  
Note: http://dx.doi.org/10.1142/S0219720007002631.
       

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Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In JBCB, Vol. 4(4):807-832, 2006.  
Keywords: explicit network, from distances, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/dist_ugn7_JBCB2006.pdf.
       
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Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson and Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. In JBCB, Vol. 4(1):59-74, 2006.  
Note: http://www.df.lth.se/~jj/Publications/forb_triplets7_JBCB2006.pdf.
       
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Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In TCS, Vol. 363(1):60-68, 2006. 1 comment  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt8_TCS2006.pdf.
       
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Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):1098-1121, 2006. 1 comment  
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.
       
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Arvind Gupta, Ján Manuch, Xiaohong Zhao and Ladislav Stacho. Characterization of the existence of galled-tree networks. In JBCB, Vol. 4(6):1309-1328, 2006.  
Keywords: characterization, galled tree.
Note: http://www.pims.math.ca/~manuch/papers/characterization_JBCB2006.pdf.
       

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Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In MFCS05, Vol. 3618:224-235 of LNCS, springer, 2005.  
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/11549345_20.
       

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Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In TCS, Vol. 335(1):93-107, 2005.  
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf.
       
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Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson and Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. In APBC05, Pages 339-348, 2005.  
Note: https://dflund.se/~jj/Publications/forb_triplets4_APBC2005.pdf.
       

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Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265-280 of LNCS, springer, 2005.  
Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.
       

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Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In ISAAC04, Vol. 3341:581-593 of LNCS, springer, 2005.  
Keywords: dynamic programming, MASN, nested network, NP complete, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested7_ISAAC2004.pdf.
       

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Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349-358, 2005. 1 comment  
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=1070481.
       

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Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134-147 of Electronic Notes in Theoretical Computer Science, 2004.  
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.
       
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Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.  
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
       
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Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462-471 of LNCS, springer, 2004. 1 comment  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf.