Publications list            
Showing 1 - 30 (650 total)
1
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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.
       

2
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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.
       

3
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Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data. 2017.  
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.
       

4
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Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. 2017.  
Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1704.02062.
       

5
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

6
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Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.  
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.
       

7
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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.
       

8
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Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, 2017.  
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, to appear.
       

9
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Philippe Gambette, Katharina Huber and Guillaume Scholz. Bridging the gap between rooted and unrooted phylogenetic networks. In BMB, 2017.  
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, to appear.
       

10
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Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.  
Keywords: approximation, explicit network, from binets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
       

11
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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.
       

12
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Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.  
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.
       

13
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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.
       

14
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Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.  
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.
       

15
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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, Vol. 74(7):1729-1751, 2017.  
Keywords: galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1007/s00285-016-1068-3.
       

16
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Gabriel Cardona and Joan Carles Pons. Reconstruction of LGT networks from tri-LGT-nets. In JOMB, 2017.  
Keywords: explicit network, From tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: to appear.
       

17
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Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.  
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.
       

18
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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, SPR distance.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

19
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Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.  
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
       

20
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Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.  
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

21
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Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017.  
Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network.
Note: http://arxiv.org/abs/1509.06104v1.
       

22
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Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.  
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
       

23
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Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, 2017.  
Keywords: from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf, to appear.
       

24
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Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.  
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.
       

25
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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.
       

26
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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.
       

27
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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.
       

28
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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.
       

29
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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.
       

30
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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/.