Search results for ' Methods in Molecular Biology ' :
    141 matches found.
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Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21 .
       
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Monika Balvociute, Andreas Spillner and Vincent Moulton. FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383-396, 2014.  
Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network.
Note: http://dx.doi.org/10.1093/sysbio/syu001.
       
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3
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Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.  
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.
       
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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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Robert G. Beiko and Mark A. Ragan. Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction. In Horizontal Gene Transfer, Vol. 532:241-256 of Methods in Molecular Biology, 2009.  
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_14.
       
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Maria S. Poptsova. Testing Phylogenetic Methods to Identify Horizontal Gene Transfer. In Horizontal Gene Transfer, Pages 227-240, 2009.  
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_13.
       
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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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8
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James B. Whitfield, Sydney A. Cameron, Daniel H. Huson and Mike Steel. Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees. In Systematic Biology, Vol. 57(6):939-947, 2008.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork.
Note: http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Z-closure%20SystBiol.pdf.
       

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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Extended Newick: It is Time for a Standard Representation. In BMCB, Vol. 9:532, 2008.  
Keywords: evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization.
Note: http://bioinfo.uib.es/media/uploaded/bmc-2008-enewick-sub.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 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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David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014.  
Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
       

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Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.  
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
       

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Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013.  
Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
       
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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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David A. Morrison. Phylogenetic networks are fundamentally different from other kinds of biological networks. In WenJun Zhang editor, Network Biology: Theories, Methods and Applications, Chapter 2, Nova Publishers, 2013.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny.
       

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Alberto Apostolico, Matteo Comin, Andreas W. M. Dress and Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):1-10, 2013.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet.
Note: http://dx.doi.org/10.1186/1748-7188-8-7.
       
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Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.  
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
       
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Daniel H. Huson and Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):1061-1067, 2012.  
Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
       
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20
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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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Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.  
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.
       
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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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Daniel H. Huson. Drawing Rooted Phylogenetic Networks. In TCBB, Vol. 6(1):103-109, 2009.  
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization.
Note: http://dx.doi.org/10.1109/TCBB.2008.58.
       
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24
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Vincent Moulton and Katharina Huber. Split Networks. A tool for exploring complex evolutionary relationships in molecular data. In Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme editors, The Phylogenetic Handbook, Cambridge University Press, 2009.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
       

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Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.  
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.
       
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26
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Tobias Kloepper and Daniel H. Huson. Drawing explicit phylogenetic networks and their integration into SplitsTree. In BMCEB, Vol. 8(22), 2008.  
Keywords: explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://dx.doi.org/10.1186/1471-2148-8-22.
       
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27
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Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.  
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://tobias-lib.ub.uni-tuebingen.de/volltexte/2008/3336/.
       

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Stefan Grünewald, Andreas Spillner, Kristoffer Forslund and Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284-295 of LNCS, springer, 2008.  
Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_24.
       
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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.
       

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Daniel H. Huson and Tobias Kloepper. Beyond Galled Trees - Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211-225 of LNCS, springer, 2007.  
Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-71681-5_15, errata..
       

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Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007.  
Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software.
Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.
       

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Tamir Tuller and Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. 2007.  
Keywords: lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf.
       

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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.
       

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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.
       

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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.
       

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Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005. 1 comment  
Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network.
Note: http://dx.doi.org/10.1109/BIBE.2005.19.
       
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Insa Cassens, Patrick Mardulyn and Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363-372, 2005.  
Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software.
Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.
       

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David Bryant and Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255-265, 2004.  
Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.
       
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Andreas W. M. Dress and Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109-115, 2004.  
Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.
       
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Daniel H. Huson, Tobias Dezulian, Tobias Kloepper and Mike Steel. Phylogenetic Super-Networks from Partial Trees. In TCBB, Vol. 1(4):151-158, 2004.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork.
Note: http://hdl.handle.net/10092/3177.
       
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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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Daniel H. Huson. What If I Don't Have a Tree? Split Decomposition and Related Models. In Current Protocols in Bioinformatics, Vol. Unit 6.7, 2003.  
Keywords: abstract network, phylogenetic network, Program SplitsTree, software, split decomposition, split network.
Note: http://dx.doi.org/10.1002/0471250953.bi0607s01.
       

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Vassily A. Lyubetsky and Vladimir V. V´yugin. Methods of horizontal gene transfer determination using phylogenetic data. In In Silico Biology, Vol. 3(1-2):17-31, 2003.  
Note: http://www.bioinfo.de/isb/2003030003/.
       

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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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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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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.
       

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Vincent Berry and David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 59-68, 1999.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.
       

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Daniel H. Huson. SplitsTree: analyzing and visualizing evolutionary data. In BIO, Vol. 14(1):68-73, 1998.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, split network.
Note: http://bioweb.pasteur.fr/docs/doc-gensoft/splitstree/splitstree.ps.
       

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Andreas W. M. Dress, Daniel H. Huson and Vincent Moulton. Analyzing and visualizing distance data using SplitsTree. In DAM, Vol. 71(1):95-109, 1996.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://bibiserv.techfak.uni-bielefeld.de/splits/splits.pdf.
       

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Daniel H. Huson and Rainer Wetzel. Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2. 1995.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, software, split network, visualization.
Note: Technical report, http://citeseer.ist.psu.edu/173442.html.
       

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Laurent Excoffier and Peter E. Smouse. Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony. In GEN, Vol. 136:343-359, 1994.  
Keywords: from distances, minimum spanning network, phylogenetic network, phylogeny, Program Arlequin, reconstruction, software.
Note: http://www.genetics.org/cgi/content/abstract/136/1/343.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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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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.
       

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Katharina Huber, Leo van Iersel, Vincent Moulton and Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102-111, 2015.  
Keywords: explicit network, from network, from rooted trees, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1093/sysbio/syu076.
       

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Andrew R. Francis and Mike Steel. Which phylogenetic networks are merely trees with additional arcs? In Systematic Biology, Vol. 64(5):768-777, 2015.  
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, tree-based network.
Note: http://arxiv.org/abs/1502.07045.
       

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Fabio Pardi and Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable. In PLoS Computational Biology, Vol. 11(4), 2015.  
Keywords: branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pcbi.1004135.
       

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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.  
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.
       

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Vladimir Makarenkov, Alix Boc and Pierre Legendre. A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers. In Fuad Aleskerov, Boris Goldengorin and Panos M. Pardalos editors, Clusters, Orders, and Trees: Methods and Applications, Vol. 92 of Springer Optimization and Its Applications, Springer, 2014.  
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction.
       

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Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.  
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.
       
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Yun Yu. Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. PhD thesis, Rice University, U.S.A., 2014.  
Keywords: hybridization, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://hdl.handle.net/1911/77583.
       

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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.
       

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Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.  
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       
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Juan Wang, Maozu Guo, Linlin Xing, Kai Che, Xiaoyan Liu and Chunyu Wang. BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees. In Gene, Vol. 527(1):344-351, 2013.  
Keywords: explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software.
       
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Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry and Celine Scornavacca. Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods. In PLoS ONE, Vol. 8(10):e73667, 2013.  
Keywords: duplication, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, Program GraphDTL, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pone.0073667.
       
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Gergely J. Szöllösi, Eric Tannier, Nicolas Lartillot and Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.  
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.
       
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Gergely J. Szöllösi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier and Vincent Daubin. Efficient Exploration of the Space of Reconciled Gene Trees. In Systematic Biology, Vol. 62(6):901-912, 2013.  
Keywords: duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction.
Note: http://arxiv.org/abs/1306.2167.
       
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Celine Scornavacca, Simone Linz and Benjamin Albrecht. A fi rst step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1109.3268.
       
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Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012.  
Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model.
Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.
       
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Benjamin Albrecht, Celine Scornavacca, Alberto Cenci and Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191-197, 2012.  
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
       
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Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012.  
Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software.
Note: http://arxiv.org/abs/1205.3417.
       
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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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Shlomo Moran, Sagi Snir and Wing-Kin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. In ACM Transactions on Algorithms, Vol. 7(4), 2011.  
Keywords: evaluation, galled tree, phylogenetic network.
Note: http://www.cs.technion.ac.il/~moran/r/PS/gnets-TOA-7Feb2007.pdf.
       
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Klaus Schliep. Phangorn: Phylogenetic analysis in R. In Bioinformatics, Vol. 27(4):592-593, 2011.  
Keywords: abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network.
Note: http://dx.doi.org/10.1093/bioinformatics/btq706.
       
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Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.  
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.
       
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Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248-i256 of BIO, 2011.  
Keywords: from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
       
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81
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Philippe Gambette. Méthodes combinatoires de reconstruction de réseaux phylogénétiques. PhD thesis, Université Montpellier 2, France, 2010.  
Keywords: abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy.
Note: http://tel.archives-ouvertes.fr/tel-00608342/en/.
       

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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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Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.  
Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
       
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Joel Velasco and Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675-687, 2010.  
Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf.
       
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Alix Boc, Hervé Philippe and Vladimir Makarenkov. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. In Systematic Biology, Vol. 59(2):195-211, 2010.  
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf.
       

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Erik W. Bloomquist and Marc A. Suchard. Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework. In Systematic Biology, Vol. 59(1):27-41, 2010.  
Note: http://dx.doi.org/10.1093/sysbio/syp076.
       

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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.
       

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Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010, 2010.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
       
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Stefan Grünewald, Vincent Moulton and Andreas Spillner. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. In DAM, Vol. 157(10):2325-2334, 2009.  
Keywords: abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://dx.doi.org/10.1016/j.dam.2008.06.038.
       
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Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009.  
Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction.
Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.
       

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Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette and Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85-i93 of BIO, 2009.  
Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/.
       
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Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009.  
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://www.ic0.net/thesis-martin-final.pdf.
       

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Klaus Schliep. Some applications of statistical phylogenetics. PhD thesis, Massey University, New Zealand, 2009.  
Keywords: abstract network, phylogenetic network, Program Phangorn, reconstruction, split network.
Note: http://muir.massey.ac.nz/handle/10179/931.
       

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Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing Level-2 Phylogenetic Networks from Triplets. In TCBB, Vol. 6(4):667-681, 2009.  
Note: http://www.win.tue.nl/~liersel/level2full.pdf.
       

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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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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.
       

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Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478-488, 2009.  
Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1093/sysbio/syp055.
       

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Chen Meng and Laura S. Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. In Theoretical Population Biology, Vol. 75(1):35-45, 2009.  
Keywords: bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1016/j.tpb.2008.10.004.
       
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Bui Quang Minh, Steffen Klaere and Arndt von Haeseler. Taxon Selection under Split Diversity. In Systematic Biology, Vol. 58(6):586-594, 2009.  
Keywords: abstract network, circular split system, diversity, from network, phylogenetic network, split network.
Note: http://dx.doi.org/10.1093/sysbio/syp058.
       
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100
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Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing level-2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450-462 of LNCS, springer, 2008.  
Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction.
Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
       
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Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.  
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.
       

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Daniel H. Huson and Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296-305 of LNCS, springer, 2008.  
Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.
       
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Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In TCS, Vol. 401:153-164, 2008.  
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf.
       

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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 child network, tree sibling network.
Note: http://dx.doi.org/10.1093/molbev/msn219.
       
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Olivier Gauthier and François-Joseph Lapointe. Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies. In Systematic Biology, Vol. 56(2):345-355, 2007.  
Keywords: consensus.
Note: http://dx.doi.org/10.1080/10635150701286549.
       
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Stefan Grünewald, Kristoffer Forslund, Andreas W. M. Dress and Vincent Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. In MBE, Vol. 24(2):532-538, 2007.  
Keywords: abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532.
       
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107
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Barbara R. Holland, Glenn Conner, Katharina Huber and Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):57-67, 2007.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215.
       
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108
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Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. In ECCB06, Vol. 23(2):e123-e128 of BIO, 2007.  
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf.
       

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Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07), 2007.  
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf.
       

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Maria S. Poptsova and J. Peter Gogarten. The power of phylogenetic approaches to detect horizontally transferred genes. In BMCEB, Vol. 7(45), 2007.  
Keywords: evaluation, from rooted trees, lateral gene transfer, Program EEEP.
Note: http://dx.doi.org/10.1186/1471-2148-7-45.
       
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Daniel H. Huson, Daniel C. Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp. Dendroscope: An interactive viewer for large phylogenetic trees. In BMCB, Vol. 8:460, 2007.  
Keywords: phylogeny, Program Dendroscope, software, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-8-460, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0903/huson/, software freely available from http://www.dendroscope.org.
       
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Patricia Buendia and Giri Narasimhan. Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples. In ISBRA07, Vol. 4463:109-120 of LNCS, springer, 2007.  
Keywords: evaluation, phylogenetic network, phylogeny, recombination, recombination detection.
Note: http://dx.doi.org/10.1007/978-3-540-72031-7_10.
       

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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.
       

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Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1186/1745-6150-2-36.
       
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Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.  
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.
       
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Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In TCBB, Vol. 3(4), 2006.  
Note: http://www.utdallas.edu/~yzhang/Homepage/Papers/prep-tcbb.pdf.
       
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Mihaela Baroni, Charles Semple and Mike Steel. Hybrids in Real Time. In Systematic Biology, Vol. 55(1):46-56, 2006.  
Keywords: agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network.
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf.
       
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Monique M. Morin and Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. In BIO, Vol. 22(15):1921-1923, 2006.  
Keywords: generation, hybridization, Program NetGen, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl191.
       
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Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.  
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.
       
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Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320-323, 2005.  
Note: http://dx.doi.org/10.1109/BIBE.2005.46.
       
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Barbara R. Holland, Frédéric Delsuc and Vincent Moulton. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. In Systematic Biology, Vol. 54(1):66-76, 2005.  
Keywords: consensus.
Note: http://hal-sde.archives-ouvertes.fr/halsde-00193050/fr/.
       
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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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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 child network, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.
       

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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 child network, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.
       

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Richard C. Winkworth, David Bryant, Peter J. Lockhart, David Havell and Vincent Moulton. Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths. In Systematic Biology, Vol. 54(1):56-65, 2005.  
Keywords: abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf.
       

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David Bryant. Extending tree models to splits networks. In Lior Pachter and Bernd Sturmfels editors, Algebraic Statistics for Computational Biology, Pages 322-334, Cambridge University Press, 2005.  
Keywords: abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf.
       

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Bastienne Vriesendorp and Freek T. Bakker. Reconstructing patterns of reticulate evolution in angiosperms: what can we do? In Taxon, Vol. 54(3):593-604, 2005.  
Note: results cited in http://library.wur.nl/wda/dissertations/dis4239.pdf.
       

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Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun and Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):13-23, 2004.  
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.
       

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Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.  
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.
       

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C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.  
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.
       

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Louigi Addario-Berry, Mike Hallett and Jens Lagergren. Towards Identifying Lateral Gene Transfer Events. In PSB03, 2003.  
Keywords: evaluation, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, reconstruction.
Note: http://www.nada.kth.se/~jensl/AHLPsb.pdf.
       

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Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret and Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003.  
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.
       

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Olivier Gauthier and François-Joseph Lapointe. A comparison of alternative methods for detecting reticulation events in phylogenetic analysis. In IFCS02, Pages 365-369, springer, 2002.  
       

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Pierre Legendre and Vladimir Makarenkov. Reconstruction of biogeographic and evolutionary networks using reticulograms. In Systematic Biology, Vol. 51(2):199-216, 2002.  
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_SB.pdf.
       

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Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. An error metric for phylogenetic networks. 2002.  
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance.
Note: Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz.
       

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Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978-982, 2001.  
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/106351501753462911.
       
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Mikkel H. Schierup and Jotun Hein. Recombination and the molecular clock. In MBE, Vol. 17(10):1578-1579, 2000.  
Note: http://www.birc.dk/Publications/Articles/Schierup_2000c.pdf.
       

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Alan R. Templeton, Keith A. Crandall and Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619-633, 2000.  
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony.
Note: http://www.genetics.org/cgi/content/abstract/132/2/619.
       

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Tao Sang and Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422-434, 2000.  
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/10635159950127321.
       

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Wayne P. Maddison. Gene Trees in Species Trees. In Systematic Biology, Vol. 46(3):523-536, 1997.  
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.2307/2413694.
       

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Loren H. Rieseberg and James D. Morefield. Character expression, phylogenetic reconstruction, and the detection of reticulate evolution. In P. C. Hoch and A. G. Stephenson editors, Experimental and molecular approaches to plant biosystematics, Pages 333–353, 1995.  
Keywords: hybridization, phylogeny, Program Reticlad.
Note: http://www3.botany.ubc.ca/rieseberglab/loren pubs/1995 Chapter in Experimental and Molecular approaches to Plant Biosystematics.pdf.