Posted Thu, Jun, 13,2013
Published today in Evolutionary Bioinformatics is a new rapid communication article by Jan Irvahn, Sujay Chattopadhyay, Evgeni V. Sokurenko and Vladimir N. Minin. Read more about this paper below:
Title
rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection
Abstract
Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple change-point model, one of the most sophisticated model-based phylogenetic recombination tools, available to R users. Moreover, we equip the Bayesian change-point model with a set of pre- and post- processing routines that will broaden the application domain of this recombination detection framework. Specifically, we implement an algorithm that forms the set of input trees required by multiple change-point models. We also provide functionality for checking Markov chain Monte Carlo convergence and creating estimation result summaries and graphics. Using rbrothers, we perform a comparative analysis of two Salmonella enterica genes, fimA and fimH, that encode major and adhesive subunits of the type 1 fimbriae, respectively. We believe that rbrothers, available at R-Forge: http://evolmod.r-forge.r-project.org/, will allow researchers to incorporate recombination detection into phylogenetic workflows already implemented in R.
Click here to learn more about the article, download it and comment
Posted in: Articles Published
News Categories
Thu 08 Oct, 2015
Published This Week (5th - 9th October)Thu 08 Oct, 2015
Biomarker Insights Paper Endorsed by Editor in ChiefWed 07 Oct, 2015
Interview with Professor Jamie DaviesI would like to extend my gratitude for creating the next generation of a scientific journal -- the science journal of tomorrow. The entire process bespoke of exceptional efficiency, celerity, professionalism, competency, and service.
Facebook Google+ Twitter
Pinterest Tumblr YouTube