Publications related to 'Program TCS' : TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks), using parsimony. http://darwin.uvigo.es/software/tcs.html.
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2015
1
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Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In MEE, Vol. 6(9):1110–1116, 2015.  
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.
       

2008
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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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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.
       

2006
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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.
       

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.
       

6
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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.
       

2001
7
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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.
       

2000
8
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Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.  
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.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.