Publications related to 'survey'
 
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2016
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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.
       

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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/.
       

3
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Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS-ONE, Vol. 11(11):e0165834, 2016.  
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.
       

2014
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David A. Morrison. Phylogenetic Networks: A Review of Methods to Display Evolutionary History. In Annual Research & Review in Biology, Vol. 4(10):1518-1543, 2014.  
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

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Dan Gusfield. ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, 2014.  
Keywords: ARG, explicit network, phylogenetic network, phylogeny, survey.
Note: http://mitpress.mit.edu/books/recombinatorics.
       

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Riccardo Dondi and Yuri Pirola. Beyond Evolutionary Trees. In Ming-Yang Kao editor, Encyclopedia of Algorithms, Pages 1-7, Springer, 2014.  
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

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David A. Morrison. Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics? In Systematic Biology, Vol. 63(4):628-638, 2014.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
       

2013
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Simone Linz. Reticulation. In Brenner's Encyclopedia of Genetics (Second Edition), 2013.  
Keywords: phylogenetic network, phylogeny, survey.
       

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Luay Nakhleh. Computational approaches to species phylogeny inference and gene tree reconciliation. In Trends in Ecology and Evolution, Vol. 28(12):719-728, 2013.  
Keywords: from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf.
       
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2012
10
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Andreas W. M. Dress, Katharina Huber, Jacobus Koolen, Andreas Spillner and Vincent Moulton. An Introduction to Phylogenetic Combinatorics. Cambridge University Press, 2012.  
Keywords: phylogenetic network, split network, survey.
Note: http://www.amazon.fr/Basic-Phylogenetic-Combinatorics-Andreas-Dress/dp/0521768322.
       

11
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David A. Morrison, Leo van Iersel and Steven Kelk. The Genealogical World of Phylogenetic Networks. Blog, 2012.  
Keywords: survey.
Note: http://phylonetworks.blogspot.com/.
       

2011
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Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.
       

13
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Daniel H. Huson and Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:23-35, 2011.  
Keywords: phylogenetic network, survey.
Note: http://dx.doi.org/10.1093/gbe/evq077.
       
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14
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Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.  
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
       
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15
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David A. Morrison. Introduction to Phylogenetic Networks. RJR Productions, 2011.  
Keywords: phylogenetic network, phylogeny, reconstruction, survey.
Note: http://www.rjr-productions.org/Networks/Download.html.
       

16

Miro Ferreri, Weijie Qu and Bo Han. Phylogenetic networks: A tool to display character conflict and demographic history. In African Journal of Biotechnology , Vol. 10(60):12799-12803, 2011.  
Keywords: phylogenetic network, phylogeny, survey, visualization.
       

2010
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Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.
       

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Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659-673, 2010.  
Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey.
Note: http://dx.doi.org/10.1007/s10539-010-9217-3.
       
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David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

2009
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Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization.
Note: http://dx.doi.org/10.1186/1745-6150-4-43.
       
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21
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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 child network, tree sibling network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.
       

2008
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Birgit Gemeinholzer. Phylogenetic networks. In Björn H. Junker and Falk Schreiber editors, Analysis of Biological Networks, Pages 255-282, John Wiley and Sons Ltd, 2008.  
Keywords: survey.
Note: http://www.amazon.com/gp/reader/0470041447/.
       

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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.
       

2007
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Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.  
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
       

25
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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.
       

26
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David Penny, Barbara R. Holland and Mike Hendy. Phylogenetics: Parsimony, Networks and Distance Methods. In D. Balding, M. Bishop and C. Cannings editors, Handbook of Statistical Genetics, 3rd Ed, Pages 489-532, John Wiley and Sons Ltd, 2007.  
Keywords: survey.
Note: http://www.amazon.fr/gp/reader/0470058307/ref=sib_dp_pt#reader-link.
       

2006
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Daniel H. Huson and David Bryant. Application of Phylogenetic Networks in Evolutionary Studies. In MBE, Vol. 23(2):254-267, 2006.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey.
Note: http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org.
       
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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.
       

29
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Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.  
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.
       

2005
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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.
       

2004
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C. Randal Linder and Loren H. Rieseberg. Reconstructing patterns of reticulate evolution in plants. In American Journal of Botany, Vol. 91(10):1700-1708, 2004.  
Keywords: distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance.
Note: http://www.amjbot.org/cgi/reprint/91/10/1700.pdf.
       

2002
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David Posada, Keith A. Crandall and Edward C. Holmes. Recombination in Evolutionary Genomics. In ARG, Vol. 36:75-97, 2002.  
Keywords: phylogenetic network, phylogeny, recombination, recombination detection, survey.
Note: http://dx.doi.org/10.1146/annurev.genet.36.040202.111115.
       
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2001
33
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David Posada and Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):37-45, 2001.  
Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey.
Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.
       

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Walter M. Fitch. Reticulation. In Sydney Brenner and Jeffrey H. Miller editors, Encyclopedia of Genetics, Academic Press, 2001.  
Keywords: phylogenetic network, phylogeny, survey.
       

2000
35
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François-Joseph Lapointe. How to account for reticulation events in phylogenetic analysis: A review of distance-based methods. In Journal of Classification, Vol. 17:175-184, 2000.  
Keywords: abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy.
Note: http://dx.doi.org/10.1007/s003570000016.
       

1998
36
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Roderic D.M. Page and Michael A. Charleston. Trees within trees: phylogeny and historical associations. In TEE, Vol. 13(9):356-359, 1998.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf.