Publications related to 'tree-child network'
 
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2020
1
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Andrew R. Francis, Daniel H. Huson and Mike Steel. Normalising phylogenetic networks. 2020.  
Keywords: explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network.
Note: https://arxiv.org/abs/2008.07797.
       

2
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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.
       

3
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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.
       

4
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Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020.  
Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.
       

5
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Remie Janssen, Mark Jones and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:77-92 of LNCS, Springer, 2020.  
Keywords: cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network.
       

6
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Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-Child Network Containment. In AlCoB20, Vol. 12099:93-107 of LNCS, Springer, 2020.  
Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence.
Note: https://doi.org/10.1007/978-3-030-42266-0_8.
       

7
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Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020.  
Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying.
Note: https://arxiv.org/abs/2004.02634.
       

2019
8
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Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. In AAM, Vol. 105:102-129, 2019.  
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: https://doi.org/10.1016/j.aam.2019.01.004.
       

9
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Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.  
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.
       

10
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Jonathan Klawitter and Simone Linz. On the Subnet Prune and Regraft Distance. In ELJC, Vol. 26(2):P2.3.1-23, 2019.  
Keywords: agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://arxiv.org/abs/1805.07839.
       

11
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Andreas Gunawan, Hongwei Yan and Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019.  
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network.
Note: https://arxiv.org/abs/1806.07625.
       

12
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Yukihiro Murakami, Leo van Iersel, Remie Janssen, Mark Jones and Vincent Moulton. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks. In BMB, Vol. 81:3823-3863, 2019.  
Keywords: from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network.
Note: https://doi.org/10.1007/s11538-019-00641-w.
       

13
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Juan Wang and Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):1972-1980, 2019.  
Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network.
       

14
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Janosch Döcker, Simone Linz and Charles Semple. Displaying trees across two phylogenetic networks. In TCS, Vol. 796:129-146, 2019.  
Keywords: display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1901.06612.
       

15
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Katharina Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Rooting for phylogenetic networks. 2019.  
Keywords: explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network.
Note: https://arxiv.org/abs/1906.07430.
       

16
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Gabriel Cardona, Joan Carles Pons and Celine Scornavacca. Generation of Binary Tree-Child phylogenetic networks. In PLoS Computational Biology, Vol. 15(10):e1007440.1-29, 2019.  
Keywords: enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network.
Note: https://doi.org/10.1371/journal.pcbi.1007440.
       

2018
17
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Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018.  
Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.
       

18
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Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. In JGAA, Vol. 22(2):329-355, 2018.  
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network.
Note: https://arxiv.org/abs/1707.09579
       

19
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Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.  
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.
       

20
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Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. In JTB, Vol. 446:160-167, 2018.  
Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness.
Note: https://arxiv.org/abs/1712.04223.
       

2017
21
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Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.  
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

2016
22
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Charles Semple. Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree. In BMB, Vol. 78(1):132-137, 2016.  
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.
       

23
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Magnus Bordewich and Charles Semple. Determining phylogenetic networks from inter-taxa distances. In JOMB, Vol. 73(2):283-303, 2016.  
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness.
Note: http://132.181.26.35/~c.semple/papers/BS15b.pdf.
       

24
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Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016.  
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.
       

25
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Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016.  
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://etheses.dur.ac.uk/11768/.
       

2015
26
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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.
       

27
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Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015.  
Keywords: compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network.
       

2014
28
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Paul Cordue, Simone Linz and Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):2664-2679, 2014.  
Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.
       
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29
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Adrià Alcalà Mena, Mercè Llabrés, Francesc Rosselló and Pau Rullan. Tree-Child Cluster Networks. In Fundamenta Informaticae, Vol. 134(1-2):1-15, 2014.  
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, tree-child network.
       

2012
30
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Stephen J. Willson. Tree-average distances on certain phylogenetic networks have their weights uniquely determined. In ALMOB, Vol. 7(13), 2012.  
Keywords: from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: hhttp://www.public.iastate.edu/~swillson/Tree-AverageDis10All.pdf.
       
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2010
31
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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Path lengths in tree-child time consistent hybridization networks. In Information Sciences, Vol. 180(3):366-383, 2010.  
Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: http://arxiv.org/abs/0807.0087?context=cs.CE.
       
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32
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Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010.  
Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree sibling network, tree-child network, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.
       
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33
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Leo van Iersel, Charles Semple and Mike Steel. Locating a tree in a phylogenetic network. In IPL, Vol. 110(23), 2010.  
Keywords: cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree containment, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/1006.3122.
       
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2009
34
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Comparison of tree-child phylogenetic networks. In TCBB, Vol. 6(4):552-569, 2009.  
Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/0708.3499.
       
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35
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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric. In TCBB, Vol. 6(1):46-61, 2009.  
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, tree-child network, tripartition distance.
Note: http://dx.doi.org/10.1109/TCBB.2008.70.
       
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36
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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.
       

2008
37
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356-370, 2008.  
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree-child network, tripartition distance.
Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.
       
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38
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008.  
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1186/1471-2105-9-175.
       
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39
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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008.  
Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree-child network, tripartition distance, triplet distance.
Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf.
       

40
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Miguel Arenas, Gabriel Valiente and David Posada. Characterization of reticulate networks based on the coalescent with recombination. In MBE, Vol. 25(12):2517-2520, 2008.  
Keywords: coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1093/molbev/msn219.
       
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2007
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Stephen J. Willson. Unique determination of some homoplasies at hybridization events. In BMB, Vol. 69(5):1709-1725, 2007.  
Keywords: explicit network, from network, hybridization, labeling, normal network, phylogenetic network, tree-child network.
Note: http://www.public.iastate.edu/~swillson/unique.det.pdf.
       

2005
42
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Luay Nakhleh and Li-San Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919-926 of LNCS, springer, 2005.  
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.
       

43
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Luay Nakhleh and Li-San Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:82-99 of LNCS, springer, 2005.  
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.