Publications related to 'generation'
 
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Article (Journal)
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Monique M. Morin and Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. In BIO, Vol. 22(15):1921-1923, 2006.  
Keywords: generation, hybridization, Program NetGen, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl191.
       
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Patricia Buendia and Giri Narasimhan. Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network. In BIO, Vol. 18(22):2313-2314, 2006.  
Keywords: generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl387.
       
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Miguel Arenas and David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008.  
Keywords: coalescent, generation, Program Recodon, software.
Note: http://dx.doi.org/10.1186/1471-2105-8-458.
       
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Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 2011.  
Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software.
Note: http://arxiv.org/abs/0910.4067.
       
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Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.  
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.
       
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InProceedings
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Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.  
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Note: http://dx.doi.org/10.1007/978-3-540-68552-4_21.
       
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InBook
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Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184-208, Taylor & Francis/CRC Press, 2009.  
Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree child network, tree sibling network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.
       

PhdThesis
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Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.  
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.
       

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Sha Zhu. Stochastic tree models and probabilistic modelling of gene trees of given species networks. PhD thesis, University of Canterbury, New Zealand, 2013.  
Keywords: from network, generation, phylogenetic network, phylogeny, simulation, statistical model.
Note: http://hdl.handle.net/10092/7944.
       

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Josh Voorkamp né Collins. Untangling Evolution. PhD thesis, University of Otago, New Zealand, 2014.  
Keywords: agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction.
Note: http://otago.ourarchive.ac.nz/handle/10523/4802.
       

Misc
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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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Sha Zhu, James H. Degnan and Mike Steel. Probabilistic modeling of gene trees given species networks. 2011.  
Keywords: from network, generation, phylogenetic network, phylogeny, statistical model.
Note: Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf.