Publications related to 'NeighborNet' : NeighborNet is an algorithm which produces a planar split network from a set of splits. It is integrated in the SplitsTree software.
 
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Martyn Kennedy, Barbara R. Holland, Russel D. Gray and Hamish G. Spencer. Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks. In Systematic Biology, Vol. 54(4):620-633, 2005.  
Keywords: abstract network, consensus, NeighborNet, phylogenetic network, phylogeny.
Note: http://awcmee.massey.ac.nz/people/bholland/pdf/Kennedy_etal_2005.pdf.
       

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David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005.  
Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey.
Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.
       

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David Bryant, Vincent Moulton and Andreas Spillner. Consistency of the Neighbor-Net Algorithm. In AMB, Vol. 2(8), 2007.  
Keywords: abstract network, consistency, from distances, NeighborNet.
Note: http://dx.doi.org/10.1186/1748-7188-2-8.
       
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Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004.  
Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.
       

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Dan Levy and Lior Pachter. The Neighbor-Net Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240-258, 2011.  
Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/math/0702515.
       
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Steven M. Woolley, David Posada and Keith A. Crandall. A Comparison of Phylogenetic Network Methods Using Computer Simulation. In PLoS ONE, Vol. 3(4):e1913, 2008.  
Keywords: abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition.
Note: http://dx.doi.org/10.1371/journal.pone.0001913.
       
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David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010.  
Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition.
Note: http://dx.doi.org/10.1093/molbev/msp309.
       
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Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011.  
Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.
       
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Alexey A. Morozov, Yuri P. Galachyants and Yelena V. Likhoshway. Inferring Phylogenetic Networks from Gene Order Data. In BMRI, Vol. 2013(503193):1-7, 2013.  
Keywords: abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network.
       
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Sarah Bastkowski, Andreas Spillner and Vincent Moulton. Fishing for minimum evolution trees with Neighbor-Nets. In IPL, Vol. 114(1-2):3-18, 2014.  
Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.
       
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InProceedings
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David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/3-540-45784-4_28.
       

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Lichen Bao and Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469-478 of LNCS, springer, 2008.  
Keywords: abstract network, from distances, NeighborNet, realization, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-85097-7_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.
       
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InBook
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Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006.  
Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.
       

PhdThesis
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Bastienne Vriesendorp. Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction. PhD thesis, Wageningen University, The Netherlands, 2007.  
Keywords: consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey.
Note: http://library.wur.nl/wda/dissertations/dis4239.pdf.
       

Misc
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Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. 2017.  
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.
       

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Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. 2017.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.