Phylogenetics

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable...

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it...

Derek Gatherer MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow, G11 5JR, UK Abstract Within the 230138 bp of the rat cytomegalovirus (RCMV) genome, the G+C content changes abruptly at position 142644, constituting a G+C content frontier. To the left of this...

Marc Thuillard Belimo Automation AG, CH-8340 Hinwil, Switzerland Abstract Minimum contradiction matrices are a useful complement to distance-based phylogenies. A minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix Yni,j . A matrix element corresponds to the distance from a...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Anthony Levasseur1, Pierre Pontarotti1, Olivier Poch2 and Julie D. Thompson2 1Phylogenomics Laboratory, EA 3781 Evolution Biologique, Université de Provence, 13331 Marseille, France. 2Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Molculaire et Cellulaire, (CNRS/INSERM/ULP), BP 10142, 67404 Illkirch Cedex, France. Abstract The...

Magnus Karlsson and Jan Stenlid Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, P.O. 7026, SE-75007, Uppsala, Sweden. Abstract Gene duplication and loss play an important role in the evolution of novel functions and for shaping an organism’s gene content. Recently, it was suggested that...

Mareike Fischer and Mike Steel Allan Wilson Centre for Molecular Ecology and Evolution, Biomathematics Research Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. Abstract The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of ‘gaps’ (missing transitional stages)...

Sanjukta Aich and Louis T.J. Delbaere Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada. Abstract: Phosphoenolpyruvate carboxykinase (PCK) is the key enzyme to initiate the gluconeogenic pathway in vertebrates, yeast, plants and most bacteria. Nucleotide specificity divided all...

Marc Thuillard Belimo Automation AG, CH-8340 Hinwil, Switzerland.Abstract: Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance…

Robin G. Allaby1 and Mathew Woodwark2 1Warwick HRI, University of Warwick, Wellesbourne, CV35 9EF, UK. 2Cambridge Antibody Technology Ltd., Milstein Building, Granta Park, Cambridge CB1 6GH, UK.Abstract: A novel high throughput phylogenomic analysis (HTP) was applied to the rhodopsin G-protein coupled receptor (GPCR) family. Instances of phylogenetic mosaicism between receptors...

Mike Steel1, Aki Mimoto2 and Arne Ø. Mooers2, 3 1Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand. 2IRMACS, Simon Fraser University, Burnaby, Canada. 3Institute for Advanced Study, Berlin, Germany. Abstract: If predictions for species extinctions hold, then the ‘tree of life’ today may be quite different to that in...

Simon Creer School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom.Abstract: Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently...

Duhong Chen1, Oliver Eulenstein1, David Fernández-Baca1 and J.Gordon Burleigh2 1Department of Computer Science, Iowa State University, Ames, IA 50011, U.S.A. 2Section of Evolution and Ecology, University of California, Davis, CA 95616, U.S.A.; Current Address, NESCent, Durham, NC 27705, U.S.A.Abstract: The utility of the matrix representation with flipping (MRF) supertree method...

Xuhua Xia Department of Biology, University of Ottawa,Ottawa, Ontario, Canada.Abstract: I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are...

Michael Höhl1,2, Isidore Rigoutsos2,3 and Mark A. Ragan1,2 1Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Aus tralia. 2Australian Research Council Centre in Bioinformatics. 3Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, NY 10598, U.S.A.Abstract: We have developed an alignment-free method that...

Vivek Jayaswal1, Lars S. Jermiin2, John Robinson3 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia; Sydney University Biological Informatics and Technology Centre, University of Sydney, NSW 2006, Australia. 2School of Biological Sciences, University of Sydney, NSW 2006, Australia; Sydney University Biological Informatics and Technology Centre, University of...

Toni Gabaldón Bioinformatics Department, Centro de Investigación Principe FelipeAbstract: The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics...

Ross H Crozier1, Lisa J Dunnett2, Paul-Michael Agapow3 1School of Tropical Biology, James Cook University, Townsville, Queensland, Australia. 2School of Information Technology, James Cook University, Townsville, Queensland, Australia. 3VieDigitale Ltd, 20 Matthias Ct., 119 Church Road, Richmond, United Kingdom.Abstract: Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize...

Tanja Gernhard1, Daniel Ford2, Rutger Vos3 and Mike Steel4 1Department of Mathematics, Kombinatorische Geometrie (M9), TU München, Boltzmannstr. 3, 85747 Garching, Germany. 2Department of Mathematics, Stanford University, U.S.A. 3Department of Biological Sciences, Simon Fraser University, Vancouver, Canada. 4Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.Abstract: The reconstruction of large...

Jason T. L. Wang1, Huiyuan Shan2, Dennis Shasha3 and William H. Piel4 1Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ, USA; 2Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ, USA; 3Courant Institute of Mathematical Sciences, New York University, New York,...

Daniel P. Faith The Australian Museum, 6 College St., Sydney, NSW, Australia, 2010.Abstract: A recent paper in this journal (Faith and Baker, 2006) described bio-informatics challenges in the application of the PD (phylogenetic diversity) measure of Faith (1992a), and highlighted the use of the root of the phylogenetic tree, as...

Daniel P. Faith1, Andrew M. Baker2 1The Australian Museum, 6 College St., Sydney, NSW, 2010; 2Queensland University of Technology, School of Natural Resource Sciences, Gardens Point Campus, 2 George Street, GPO Box 2434, Brisbane, Queensland, 4001, AustraliaAbstract: Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A...

Daniel L. Rabosky Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701, U.S.A.Abstract: Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a...

Chunghau Lee1, Sigal Blay3, Arne Ø. Mooers3, Ambuj Singh1, Todd H. Oakley2,4 1Department of Computer Science; 2Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106 USA. 3Department of Biological Sciences and IRMACS, 8888 University Drive, Simon Fraser University, Burnaby, BC V5A 1S6 Canada.Abstract: Continuously varying...

Matthew Spencer1, Edward Susko1, and Andrew J. Roger2 1Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. 2Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.Abstract: The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic...

Laurent Gatto, Daniele Catanzaro and Michel C. Milinkovitch Laboratory of Evolutionary Genetics, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, CP300, rue Jeener et Brachet 12, 6041 Gosselies, Belgium.Abstract: The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny...

Edward SuskoGenome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada.Abstract: Many of the estimated topologies in phylogenetic studies are presented with the bootstrap support for each of the splits in the topology indicated. If phylogenetic estimation is unbiased, high bootstrap support for a split suggests that...

Abdoulaye Baniré Diallo1, François-Joseph Lapointe2 and Vladimir Makarenkov1 1Département d’informatique, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal (Québec), H3C 3P8, Canada. banire(at)lacim.uqam.ca; makarenkov.vladimir(at)uqam.ca 2Département de sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal (Québec), H3C 3J7, Canada. francois-joseph.lapointe(at)umontreal.caAbstract: In this article we address the problem...