Search results for ' ARG ' :
    20 matches found.
1
photophotophotophoto
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.
       

2
photophotophotophotophoto
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, 2016.  
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
Note: to appear.
       

3
photo
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.
       

4
photo
Willem Sonke. Reconstructing a level-1-network from quartets. 2013.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program Fylogenetica, reconstruction, software, visualization.
Note: http://alexandria.tue.nl/extra1/afstversl/wsk-i/sonke2013.pdf.
       

5
photophoto
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.
       

6
photophotophoto
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.
       
Toggle abstract
7
photophotophotophotophotophoto
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.
       
Toggle abstract
8
photophotophotophotophoto
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles Langley and Yufeng Wu. Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):1273-1286, 2007.  
Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2007.0096.
       
Toggle abstract
9
photophotophoto
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.
       

10
photophotophoto
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/.
       
Toggle abstract
11
photophotophoto
Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.  
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
       

12
photophoto
Yun S. Song and Jotun Hein. Constructing Minimal Ancestral Recombination Graphs. In JCB, Vol. 12(2):147-169, 2005.  
Keywords: ARG, minimum number, recombination.
Note: http://www.eecs.berkeley.edu/~yss/Pub/SH-JCB05.pdf.
       

13
photophotophoto
Yun S. Song, Yufeng Wu and Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413-i422 of BIO, 2005.  
Keywords: minimum number, Program HapBound, Program SHRUB, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
       
Toggle abstract
14
photophotophoto
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.
       

15
photophoto
Vineet Bafna and Vikas Bansal. The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. In TCBB, Vol. 1(2):78-90, 2004.  
Keywords: ARG, bound, minimum number, phylogeny, recombination.
Note: http://www-cse.ucsd.edu/users/vbafna/pub/tcbb04.pdf.
       
Toggle abstract
16
photophotophoto
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.
       
Toggle abstract
17
photo
Barbara R. Holland. Evolutionary analyses of large data sets: Trees and beyond. PhD thesis, Massey University, New Zealand, 2001.  
Keywords: median network, split.
Note: http://mro.massey.ac.nz/handle/10179/2078.
       

18
photophoto
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.
       

19
photophoto
Paul Marjoram and Robert C. Griffiths. Ancestral inference from samples of DNA sequences with recombination. In JCB, Vol. 3(4):479-502, 1996.  
Keywords: ARG, phylogenetic network, phylogeny, statistical model.
Note: http://www.math.canterbury.ac.nz/~r.sainudiin/recomb/JCB_paper.pdf.
       

20
photophoto
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.