Who is Who in Phylogenetic Networks

Publications related to 'Program Arlequin' : The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. In particular, Arlequin implements a Minimum Spanning Network algorithm to embed the set of all minimum spanning trees computed from a distance matrix of haplotypes (http://cmpg.unibe.ch/software/arlequin3/).   Order by:   Type | Year

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Associated keywords

abstract-network distance-between-networks evaluation from-distances from-unrooted-trees haplotype-network hybridization lateral-gene-transfer likelihood median-network MedianJoining minimum-spanning-network NeighborNet netting parsimony phylogenetic-network phylogeny Program-Arlequin Program-CombineTrees Program-Network Program-Pyramids Program-Reticlad Program-SHRUB Program-SplitsTree Program-T-REX Program-TCS Program-WeakHierarchies pyramid reconstruction reticulogram software split split-decomposition split-network statistical-parsimony survey weak-hierarchy

Article (Journal)

1 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.         2 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.         3 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.         4 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 "Background: We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches (neighbor-joining and maximum parsimony) in the presence and absence of recombination. Principal Findings: In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the subtitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths. Conclusions: Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future. © 2008 Woolley et al."

InBook

5 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.