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rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.

Titlerbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.
Publication TypeJournal Article
Year of Publication2013
AuthorsIrvahn J, Chattopadhyay S, Sokurenko EV, Minin VN
JournalEvolutionary bioinformatics online
Date Published2013

<p>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:, will allow researchers to incorporate recombination detection into phylogenetic workflows already implemented in R.</p>

Alternate JournalEvol. Bioinform. Online