Who is Who in Phylogenetic Networks

Publications of Year 2001

Article (Journal)

1 Vladimir Makarenkov. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. In BIO, Vol. 17(7):664-668, 2001. Keywords: phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf.         2 Korbinian Strimmer, Carsten Wiuf and Vincent Moulton. Recombination Analysis Using Directed Graphical Models. In MBE, Vol. 18(1):97-99, 2001. Keywords: recombination, statistical model. Note: http://mbe.oxfordjournals.org/cgi/content/full/18/1/97.         3 Katharina Huber, Vincent Moulton, Peter J. Lockhart and Andreas W. M. Dress. Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks. In MPE, Vol. 19(2):302-310, 2001. Keywords: abstract network, median network, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1006/mpev.2001.0935.         Toggle abstract "Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not tree-like. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins. © 2001 Academic Press." 4 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.         Toggle abstract [No abstract available] 5 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.

InProceedings

6 Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Hereditarily Optimal Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them? In Proceedings of the Euroconference on Algebraic Combinatorics and Applications (Alcoma'99), Pages 110-117, springer, 2001. Keywords: abstract network, from distances, optimal realization, phylogenetic network. Note: http://www.math.uni-bielefeld.de/fsp-math/Preprints/139.pdf.         7 Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. In RECOMB01, Pages 141-148, 2001. Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, Program McKiTscH, reconstruction. Note: http://dx.doi.org/10.1145/369133.369188.         8 Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001. Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction. Note: http://dx.doi.org/10.1145/372202.372271.

InBook

9 Walter M. Fitch. Reticulation. In Sydney Brenner and Jeffrey H. Miller editors, Encyclopedia of Genetics, Academic Press, 2001. Keywords: phylogenetic network, phylogeny, survey.

PhdThesis

10 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.