Publications list            
Showing 1 - 30 (638 total)
1
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Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. 2017.  
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898, to appear.
       

2
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Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. 2017.  
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.06364.
       

3
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Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. 2017.  
Keywords: bound, distance between networks, from network, NNI distance, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.
       

4
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Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.  
Keywords: explicit network, FPT, from binets, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
       

5
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Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.  
Keywords: compressed network, Number of vertices, phylogenetic network, phylogeny.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.
       

6
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Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.  
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment..
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.
       

7
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Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016.  
Keywords: phylogenetic network, phylogeny, statistical model.
Note: http://arxiv.org/abs/1606.07160.
       

8
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Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. 2016.  
Keywords: circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.
       

9
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Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.  
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
       

10
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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.
       

11
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Andrew R. Francis, Charles Semple and Mike Steel. New Characterisations of Tree-Based Networks and Proximity Measures. 2016.  
Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1611.04225.
       

12
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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/.
       

13
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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, enumeration, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.
       

14
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Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.  
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.
       

15
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Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016.  
Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization.
Note: http://arxiv.org/abs/1609.00755.
       

16
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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 .
       

17
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Dan Graur. Reticulate evolution and phylogenetic networks. In Molecular and Genome Evolution, Chapter 6, Sinauer, 2016.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf.
       

18
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Mike Steel. Introduction to phylogenetic networks. In Phylogeny: Discrete and Random Processes in Evolution, Vol. 89 of CBMS-NSF Regional Conference Series in Applied Mathematics, Chapter Chapter 10, SIAM, 2016.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
Note: http://bookstore.siam.org/cb89/.
       

19
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Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.  
Keywords: branch length, evaluation, explicit network, phylogenetic network, phylogeny, statistical model, tree-based network.
Note: http://arxiv.org/abs/1606.07350.
       

20
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Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB2016, Vol. 9649:266 of LNBI, Springer, 2016.  
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: http://arxiv.org/abs/1507.02119.
       

21
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Stephen J. Willson. Comparing and simplifying distinct-cluster phylogenetic networks. In ACOM, Vol. 20(4):917-938, 2016.  
Keywords: distinct-cluster network, explicit network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1501.07528.
       

22
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Magnus Bordewich and Charles Semple. Reticulation-visible networks. In Advances in Applied Mathematics, Vol. 78:114-141, 2016.  
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf.
       

23
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François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.
       

24
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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.
       

25
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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 child network, tree-based network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.
       

26
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Maria Anaya, Olga Anipchenko-Ulaj, Aisha Ashfaq, Joyce Chiu, Mahedi Kaiser, Max Shoji Ohsawa, Megan Owen, Ella Pavlechko, Katherine St. John, Shivam Suleria, Keith Thompson and Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016.  
Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1602.02739.
       

27
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Juan Wang. A Metric on the Space of Partly Reduced Phylogenetic Networks. In BMRI, Vol. 2016(7534258):1-9, 2016.  
Keywords: distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks.
Note: http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf.
       

28
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Juan Wang, Zhang Zhibin and Yanjuan Li. Constructing phylogenetic networks based on the isomorphism of datasets. In BMRI, Vol. 2016(4236858):1-7, 2016.  
Keywords: from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf.
       

29
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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.
       

30
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Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.  
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.