Who is Who in Phylogenetic Networks

Publications list	Showing 721 - 750 (752 total)

721 Hans-Jürgen Bandelt, Peter Forster, Bryan C. Sykes and Martin Richards. Mitochondrial portraits of human population using median networks. In GEN, Vol. 141:743-753, 1995. Keywords: from splits, median network, population genetics, Program Spectronet, reconstruction, visualization. Note: http://www.genetics.org/cgi/content/abstract/141/2/743.         722 Hans-Jürgen Bandelt. Combination of data in phylogenetic analysis. In PSE, Vol. Supp. 9:336-361, 1995. Keywords: from trees, phylogenetic network, phylogeny, reconstruction.         723 Hans-Jürgen Bandelt and Andreas W. M. Dress. A relational approach to split decomposition. In H.-H. Bock, W. Lenski and M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123-131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994. Keywords: characterization, from quartets, phylogenetic network, weakly compatible.         724 John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In SODA94, Pages 471-480, 1994. Keywords: from sequences, NP complete, polynomial, recombination, reconstruction. Note: http://portal.acm.org/citation.cfm?id=314626#.         725 Hans-Jürgen Bandelt. Phylogenetic Networks. In Verhandlungen des Naturwissenschaftlichen Vereins Hamburg, Vol. 34:51-71, 1994.         726 Zdenek Skála and Jan Zrzavý. Phylogenetic reticulations and cladistics: discussion of methodological concepts. In Cladistics, Vol. 10(3):305-313, 1994. Keywords: explicit network, from rooted trees, from species tree, parsimony, phylogeny. Note: http://dx.doi.org/10.1111/j.1096-0031.1994.tb00180.x.         727 Hans-Jürgen Bandelt and Andreas W. M. Dress. An order theoretic framework for overlapping clustering. In DM, Vol. 136(1-3):21-37, 1994.         Toggle abstract "Cluster analysis deals with procedures which - given a finite collection X of objects together with some kind of local dissimilarity information - identify those subcollections C of objects from X, called clusters, which exhibit a comparatively low degree of internal dissimilarity. In this note we study arbitrary mappings φ which assign to each subcollection A ⊆ X of objects its internal degree of dissimilarity φ (A), subject only to the natural condition that A ⊆ B ⊆ X implies φ (A) ̌ φ (B), and we analyse on a rather abstract, purely order theoretic level how assumptions concerning the way such a mapping φ might be constructed from local data (that is, data involving only a few objects at a time) influence the degree of overlapping observed within the resulting family of clusters, - and vice versa. Hence, unlike previous order theoretic approaches to cluster analysis, we do not restrict our attention to nonoverlapping, hierarchical clustering. Instead, we regard a dissimilarity function φ as an arbitrary isotone mapping from a finite partially ordered set I - e.g. the set P(X) of all subsets A of a finite set X - into a (partially) ordered set R - e.g. the nonnegative real numbers - and we study the correspondence between the two subsets C(φ) and D(φ) of I, formed by the elements whose images are inaccessible from above and from below, respectively. While D(φ) constitutes the local data structure from which φ can be built up, C(φ) embodies the family of clusters associated with φ. Our results imply that in case I: = P(X) and R: = R≥0 one has # D ̌ n for all Dε{lunate}D(φ) and some fixed nε{lunate}N if and only if{A figure is presented} for all C0,..., Cnε{lunate}C(φ) if and only if this holds for all subsets C0,..., Cn ⊆ X, generalizing a well-known criterion for n-conformity of hypergraphs as well as corresponding results due to Batbedat, dealing with the case n = 2. © 1994." 728 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.         729 Arndt von Haeseler and Gary A. Churchill. Network models for sequence evolution. In JME, Vol. 37(1):77-85, 1993. Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://dx.doi.org/10.1007/BF00170465.         730 Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993. Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software. Note: http://dx.doi.org/10.1007/BF00182187.         731 Joaquin Dopazo, Andreas W. M. Dress and Arndt von Haeseler. Split decomposition: a new technique to analyse viral evolution. In PNAS, Vol. 90:10320-10324, 1993. Keywords: abstract network, phylogenetic network, phylogeny, split, split decomposition, split network, visualization. Note: http://dx.doi.org/10.1073/pnas.90.21.10320.         732 Hans-Jürgen Bandelt. Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies. 1992. Keywords: characterization, clustering, from distances, pyramid, weak hierarchy. Note: Mathematisches Seminar, Universität Hamburg.         733 Hans-Jürgen Bandelt and Andreas W. M. Dress. A canonical decomposition theory for metrics on a finite set. In Advances in Mathematics, Vol. 92(1):47-105, 1992. Keywords: abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible.         Toggle abstract "We consider specific additive decompositions d = d1 + ... + dn of metrics, defined on a finite set X (where a metric may give distance zero to pairs of distinct points). The simplest building stones are the slit metrics, associated to splits (i.e., bipartitions) of the given set X. While an additive decomposition of a Hamming metric into split metrics is in no way unique, we achieve uniqueness by restricting ourselves to coherent decompositions, that is, decompositions d = d1 + ... + dn such that for every map f:X → R with f(x) + f(y) ≥ d(x, y) for all x, y ε{lunate} X there exist maps f1, ..., fn: X → R with f = f1 + ... + fn and fi(x) + fi(y) ≥ di(x, y) for all i = 1,..., n and all x, y ε{lunate} X. These coherent decompositions are closely related to a geometric decomposition of the injective hull of the given metric. A metric with a coherent decomposition into a (weighted) sum of split metrics will be called totally split-decomposable. Tree metrics (and more generally, the sum of two tree metrics) are particular instances of totally split-decomposable metrics. Our main result confirms that every metric admits a coherent decomposition into a totally split-decomposable metric and a split-prime residue, where all the split summands and hence the decomposition can be determined in polynomial time, and that a family of splits can occur this way if and only if it does not induce on any four-point subset all three splits with block size two. © 1992." 734 Lucinda A. McDade. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. In Evolution, Vol. 46(5):1329-1346, 1992. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny. Note: http://www.jstor.org/stable/2409940.         735 Hans-Jürgen Bandelt and Andreas W. M. Dress. Split Decomposition: A new and useful approach to phylogenetic analysis of distance data. In MPE, Vol. 1(3):242-252, 1992. Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split decomposition, split network. Note: http://dx.doi.org/10.1016/1055-7903(92)90021-8.         Toggle abstract "In order to analyze the structure inherent to a matrix of dissimilarities (such as evolutionary distances) we propose to use a new technique called split decomposition. This method accurately dissects the given dissimilarity measure as a sum of elementary "split" metrics plus a (small) residue. The split summands identify related groups which are susceptible to further interpretation when casted against the available biological information. Reanalysis of previously published ribosomal RNA data sets using split decomposition illustrate the potential of this approach. © 1992." 736 Jotun Hein. Reconstructing evolution of sequences subject to recombination using parsimony. In MBIO, Vol. 98(2):185-200, 1990. Note: http://dx.doi.org/10.1016/0025-5564(90)90123-G.         Toggle abstract "The parsimony principle states that a history of a set of sequences that minimizes the amount of evolution is a good approximation to the real evolutionary history of the sequences. This principle is applied to the reconstruction of the evolution of homologous sequences where recombinations or horizontal transfer can occur. First it is demonstrated that the appropriate structure to represent the evolution of sequences with recombinations is a family of trees each describing the evolution of a segment of the sequence. Two trees for neighboring segments will differ by exactly the transfer of a subtree within the whole tree. This leads to a metric between trees based on the smallest number of such operations needed to convert one tree into the other. An algorithm is presented that calculates this metric. This metric is used to formulate a dynamic programming algorithm that finds the most parsimonious history that fits a given set of sequences. The algorithm is potentially very practical, since many groups of sequences defy analysis by methods that ignore recombinations. These methods give ambiguous or contradictory results because the sequence history cannot be described by one phylogeny, but only a family of phylogenies that each describe the history of a segment of the sequences. The generalization of the algorithm to reconstruct gene conversions and the possibility for heuristic versions of the algorithm for larger data sets are discussed. © 1990." 737 Patrice Bertrand and Edwin Diday. Une généralisation des arbres hiérarchiques~: les représentations pyramidales. In Revue de Statistique Appliquée, Vol. 38(3):53-78, 1990. Note: http://www.numdam.org/item?id=RSA_1990__38_3_53_0.         738 Hans-Jürgen Bandelt and Andreas W. M. Dress. Weak hierarchies associated with similarity measures: an additive clustering technique. In BMB, Vol. 51:113-166, 1989. Keywords: abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy. Note: http://dx.doi.org/10.1007/BF02458841.         Toggle abstract "A new and apparently rather useful and natural concept in cluster analysis is studied: given a similarity measure on a set of objects, a sub-set is regarded as a cluster if any two objects a, b inside this sub-set have greater similarity than any third object outside has to at least one of a, b. These clusters then form a closure system which can be described as a hypergraph without triangles. Conversely, given such a system, one may attach some weight to each cluster and then compose a similarity measure additively, by letting the similarity of a pair be the sum of weights of the clusters containing that particular pair. The original clusters can be reconstructed from the obtained similarity measure. This clustering model is thus located between the general additive clustering model of Shepard and Arabie (1979) and the standard hierarchical model. Potential applications include fitting dendrograms with few additional nonnested clusters and simultaneous representation of some families of multiple dendrograms (in particular, two-dendrogram solutions), as well as assisting the search for phylogenetic relationships by proposing a somewhat larger system of possibly relevant "family groups", from which an appropriate choice (based on additional insight or individual preferences) remains to be made. © 1989 Society for Mathematical Biology." 739 Patrice Bertrand. Étude de la représentation pyramidale. PhD thesis, Université de Paris-Dauphine, France, 1986. Keywords: abstract network, pyramid.         740 Alain Guénoche. Graphical Representation of a Boolean Array. In Computers and the Humanities, Vol. 20(4):277-281, 1986. Keywords: from splits, median network, reconstruction. Note: http://dx.doi.org/10.1007/BF02400118.         Toggle abstract "In this paper, we represent a boolean array of data with a median connected graph. Vertices are the different lines of the array plus virtual monomials, and an edge links two vertices that are different for only one variable. We describe an algorithm to compute this graph, that is an exact representation of the symmetrical difference distance between lines, and we show an application to Bronze age pins. © 1986 Paradigm Press, Inc." 741 Ingo Althöfer. On optimal realizations of finite metric spaces by graphs. In Discrete and Computational Geometry, Vol. 3(1):103-122, 1986. Keywords: NP complete, optimal realization, realization. Note: http://dx.doi.org/10.1007/BF02187901.         Toggle abstract "Graph realizations of finite metric spaces have widespread applications, for example, in biology, economics, and information theory. The main results of this paper are: 1. Finding optimal realizations of integral metrics (which means all distances are integral) is NP-complete. 2. There exist metric spaces with a continuum of optimal realizations. Furthermore, two conditions necessary for a weighted graph to be an optimal realization are given and an extremal problem arising in connection with the realization problem is investigated. © 1988 Springer-Verlag New York Inc." 742 Victoria A. Funk. Phylogenetic patterns and hybridization. In Annals of the Missouri Botanical Garden, Vol. 72(4):681-715, 1985. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny. Note: http://www.jstor.org/stable/2399220.         743 Patrice Bertrand and Edwin Diday. A visual representation of the compatibility between an order and a dissimilarity index: the pyramids. In CSQ, Vol. 2:31-42, 1985. Keywords: pyramid.         744 Richard R. Hudson and Norman L. Kaplan. Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences. In GEN, Vol. 111:147-164, 1985. Note: http://www.genetics.org/cgi/content/abstract/111/1/147.         745 Gareth J. Nelson. Reticulation in Cladograms. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 105-111, Columbia University Press, 1983. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.         746 Hans-Erik Wanntorp. Reticulated cladograms and the identification of hybrid taxa. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 81-88, Columbia University Press, 1983. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.         747 Christopher J. Humphries. Primary data in hybrid analysis. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 89-103, Columbia University Press, 1983. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.         748 Warren H. Wagner. Reticulistics: the recognition of hybrids and their role in cladistics and classification. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 63-79, 1983. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.         749 Richard R. Hudson. Properties of the neutral allele model with intragenic recombination. In TPP, Vol. 23:183-201, 1983. Keywords: coalescent. Note: http://dx.doi.org/10.1016/0040-5809(83)90013-8, see also http://www.brics.dk/~compbio/coalescent/hudson_animator.html.         Toggle abstract "An infinite-site neutral allele model with crossing-over possible at any of an infinite number of sites is studied. A formula for the variance of the number of segregating sites in a sample of gametes is obtained. An approximate expression for the expected homozygosity is also derived. Simulation results are presented to indicate the accuracy of the approximations. The results concerning the number of segregating sites and the expected homozygosity indicate that a two-locus model and the infinite-site model behave similarly for 4Nu ≤ 2 and r ≤ 5u, where N is the population size, u is the neutral mutation rate, and r is the recombination rate. Simulations of a two-locus model and a four-locus model were also carried out to determine the effect of intragenic recombination on the homozygosity test ofWatterson (Genetics 85, 789-814; 88, 405-417) and on the number of unique alleles in a sample. The results indicate that for 4Nu ≤ 2 and r ≤ 10u, the effect of recombination is quite small. © 1983." 750 Kare Bremer and Hans-Erik Wanntorp. Hierarchy and reticulation in systematics. In Systematic Zoology, Vol. 28(4):624-627, 1979. Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny. Note: http://dx.doi.org/10.2307/2412572.