Comparative methods in R hackathon

The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased interaction within the community

ViPR: an open bioinformatics database and analysis resource for virology research

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal ‘Workbenches’ for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses

The Set-Maxima Problem: an Overview

Sorting problems have long been one of the foundations of theoretical computer science. Sorting problems attempt to learn properties of an unknown total order of a known set. We test the order by comparing pairs of elements, and through repeated tests deduce some order structure on the set. The set-maxima problem is: given a family S of subsets of a set X, produce the maximal element of each element of S. Local sorting is a sub-problem of set-maxima, when S ` i X 2 j , i.e. there exists a graph G with vertex set X and edge set S: We compare algorithms by estimating the number of comparisons needed, as a function of n = jXj; and m = jSj. In this paper, we review the information-theory lower bounds for the set-maxima and local-sorting problems. We review deterministic algorithms which have optimally solved the set-maxima problem, as a function of m;n, in settings where extra assumptions about S have been made. Also, we review randomized algorithms for local sorting and set-maxima ..

A STUDY OF CRYSTALLIZATION AND ORIENTATION MECHANISMS IN POLYETHYLENE

Abstract not availabl

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

International audienceFastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http:// www.atgc-montpellier.fr/fastme/)

Package ‘ape’

International audienc