Search results for ' AMB ' :
    46 matches found.
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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.  
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .
       

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Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. 2016.  
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: http://arxiv.org/abs/1609.00544.
       

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Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.  
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.
       

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Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, 2016.  
Keywords: galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/abs/1511.08056, to appear.
       

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Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, 2016.  
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: to appear, presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.  
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.
       

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Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.  
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.
       

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Philippe Gambette, Katharina Huber and Guillaume Scholz. Bridging the gap between rooted and unrooted phylogenetic networks. 2015.  
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.
       

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Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.  
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.
       
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Sha Zhu, James H. Degnan and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 2013.  
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://arxiv.org/abs/1303.0673.
       

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Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.
       
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Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. A short note on exponential-time algorithms for hybridization number. 2013.  
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1312.1255.
       

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Philippe Gambette and Katharina Huber. On Encodings of Phylogenetic Networks of Bounded Level. In JOMB, Vol. 65(1):157-180, 2012.  
Keywords: characterization, explicit network, from clusters, from rooted trees, from triplets, galled tree, identifiability, level k phylogenetic network, phylogenetic network, uniqueness, weak hierarchy.
Note: http://hal.archives-ouvertes.fr/hal-00609130/en/.
       
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Andreas W. M. Dress, Katharina Huber, Jacobus Koolen, Andreas Spillner and Vincent Moulton. An Introduction to Phylogenetic Combinatorics. Cambridge University Press, 2012.  
Keywords: phylogenetic network, split network, survey.
Note: http://www.amazon.fr/Basic-Phylogenetic-Combinatorics-Andreas-Dress/dp/0521768322.
       

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Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca and Leen Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):1635-1656, 2012.  
Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction.
Note: http://arxiv.org/abs/1112.5359, about the title.
       
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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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Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.
       

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Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.  
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
       
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Philippe Gambette. Méthodes combinatoires de reconstruction de réseaux phylogénétiques. PhD thesis, Université Montpellier 2, France, 2010.  
Keywords: abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy.
Note: http://tel.archives-ouvertes.fr/tel-00608342/en/.
       

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Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola and Lusheng Wang. Beyond evolutionary trees. In Natural Computing, Vol. 9(2):421-435, 2010.  
Note: http://dx.doi.org/10.1007/s11047-009-9156-6.
       
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Philippe Gambette, Vincent Berry and Christophe Paul. The structure of level-k phylogenetic networks. In CPM09, Vol. 5577:289-300 of LNCS, springer, 2009.  
Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/.
       
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Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette and Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85-i93 of BIO, 2009.  
Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/.
       
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Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing Level-2 Phylogenetic Networks from Triplets. In TCBB, Vol. 6(4):667-681, 2009.  
Note: http://www.win.tue.nl/~liersel/level2full.pdf.
       

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Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://hdl.handle.net/10092/2852.
       

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Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization.
Note: http://dx.doi.org/10.1186/1745-6150-4-43.
       
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Ali Tofigh. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden, 2009.  
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830&searchId=1.
       

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Vincent Moulton and Katharina Huber. Split Networks. A tool for exploring complex evolutionary relationships in molecular data. In Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme editors, The Phylogenetic Handbook, Cambridge University Press, 2009.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
       

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Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.  
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.
       
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Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing level-2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450-462 of LNCS, springer, 2008.  
Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction.
Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
       
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David Bryant, Vincent Moulton and Andreas Spillner. Consistency of the Neighbor-Net Algorithm. In AMB, Vol. 2(8), 2007.  
Keywords: abstract network, consistency, from distances, NeighborNet.
Note: http://dx.doi.org/10.1186/1748-7188-2-8.
       
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Hans-Jürgen Bandelt and Arne Dür. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256-271, 2007.  
Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.
       
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Olivier Gauthier. Utilisation de réseaux en analyse phylogénétique. PhD thesis, Université de Montréal, Canada, 2006.  
Note: http://igm.univ-mlv.fr/phylnet/PhylogeneticNetworks/docs/GauthierPhdThesis.pdf.
       

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David Bryant. Extending tree models to splits networks. In Lior Pachter and Bernd Sturmfels editors, Algebraic Statistics for Computational Biology, Pages 322-334, Cambridge University Press, 2005.  
Keywords: abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf.
       

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Hans-Jürgen Bandelt, Vincent Macaulay and Martin Richards. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. In MPE, Vol. 16:8-28, 2000.  
Keywords: from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf.
       
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Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.  
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.
       

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Arne Röhl. Phylogenetische Netzwerke. PhD thesis, Universität Hamburg, Germany, 1999.  
Note: http://www.sub.uni-hamburg.de/opus/volltexte/1999/53/html/Phylogenetische_Netzwerke.html.
       

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Nicholas C. Grassly and Andrew Rambaut. Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios. 1999.  
Keywords: generation, phylogenetic network, phylogeny, population genetics, Program Treevolve, software.
Note: http://evolve.zoo.ox.ac.uk/software/treevolve/manual.php.
       

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Hans-Jürgen Bandelt. Combination of data in phylogenetic analysis. In PSE, Vol. Supp. 9:336-361, 1995.  
Keywords: from trees, phylogenetic network, phylogeny, reconstruction.
       

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Hans-Jürgen Bandelt, Peter Forster, Bryan C. Sykes and Martin Richards. Mitochondrial portraits of human population using median networks. In GEN, Vol. 141:743-753, 1995.  
Keywords: from splits, median network, population genetics, Program Spectronet, reconstruction, visualization.
Note: http://www.genetics.org/cgi/content/abstract/141/2/743.
       

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Hans-Jürgen Bandelt. Phylogenetic Networks. In Verhandlungen des Naturwissenschaftlichen Vereins Hamburg, Vol. 34:51-71, 1994.  
       

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Hans-Jürgen Bandelt and Andreas W. M. Dress. An order theoretic framework for overlapping clustering. In DM, Vol. 136(1-3):21-37, 1994.  
       
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Hans-Jürgen Bandelt and Andreas W. M. Dress. A relational approach to split decomposition. In H.-H. Bock, W. Lenski and M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123-131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994.  
Keywords: characterization, from quartets, phylogenetic network, weakly compatible.
       

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Hans-Jürgen Bandelt and Andreas W. M. Dress. A canonical decomposition theory for metrics on a finite set. In Advances in Mathematics, Vol. 92(1):47-105, 1992.  
Keywords: abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible.
       
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Hans-Jürgen Bandelt and Andreas W. M. Dress. Split Decomposition: A new and useful approach to phylogenetic analysis of distance data. In MPE, Vol. 1(3):242-252, 1992.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split decomposition, split network.
Note: http://dx.doi.org/10.1016/1055-7903(92)90021-8.
       
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Hans-Jürgen Bandelt. Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies. 1992.  
Keywords: characterization, clustering, from distances, pyramid, weak hierarchy.
Note: Mathematisches Seminar, Universität Hamburg.
       

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Hans-Jürgen Bandelt and Andreas W. M. Dress. Weak hierarchies associated with similarity measures: an additive clustering technique. In BMB, Vol. 51:113-166, 1989.  
Keywords: abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy.
Note: http://dx.doi.org/10.1007/BF02458841.
       
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