Publications related to 'counting'
 
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2020
1
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Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020.  
Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.
       

2
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Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020.  
Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network.
Note: https://arxiv.org/abs/2003.08049.
       

3
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Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020.  
Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1812.08569.
       

4
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Marefatollah Mansouri. Counting General Phylogenetic networks. 2020.  
Keywords: counting, explicit network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/2005.14547.
       

5
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Marefatollah Mansouri. Combinatorial properties of phylogenetic networks. PhD thesis, Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry, 2020.  
Keywords: counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny.
Note: https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf.
       

6
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Mathilde Bouvel, Philippe Gambette and Marefatollah Mansouri. Counting Phylogenetic Networks of Level 1 and 2. In JOMB, 2020.  
Keywords: counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1909.10460, to appear.
       

2019
7
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Michael Fuchs, Bernhard Gittenberger and Marefatollah Mansouri. Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks. In Australasian Journal of Combinatorics, Vol. 73(2):385-423, 2019.  
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784.
       

2018
8
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Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018.  
Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.
       

2016
9
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Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016.  
Keywords: cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.
       

2015
10
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Colin McDiarmid, Charles Semple and Dominic Welsh. Counting phylogenetic networks. In Annals of Combinatorics, Vol. 19(1):205-224, 2015.  
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf.
       

2013
11
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Simone Linz, Katherine St. John and Charles Semple. Counting trees in a phylogenetic network is #P-complete. In SICOMP, Vol. 42(4):1768-1776, 2013.  
Keywords: counting, from network, phylogenetic network, phylogeny.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf.
       

2009
12
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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 sibling network, tree-child network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.
       

2007
13
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Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.  
Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.
       

2006
14
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Charles Semple and Mike Steel. Unicyclic networks: compatibility and enumeration. In TCBB, Vol. 3(1):84-91, 2006.  
Keywords: counting, explicit network, galled tree, unicyclic network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS06.pdf.