Available R packages:

R package: rbrothers

Developers: Jan Irvahn, Vladimir Minin

Contact: Vladimir Minin,

Overview: R package rbrothers provides easy access to recombination detection software DualBrothers and provides new functionality for pre-processing sequence data and post-processing DualBrothers output.

Source code: https://github.com/vnminin/rbrothers

Source code of DualBrothers is available here.

Installation: see Readme on github https://github.com/vnminin/rbrothers  
Tutorial: The best way to start learning how to use rbrothers is to go through our vignette rbrothers_tutorial.pdf, also available in the Sweave format: rbrothers_tutorial.Rnw.

Demos: We provide the following scripts demonstrating the usage of the package.
  1. E. coli fimH (runs for about 2 minutes):
    	  demo("fimH_example", package="rbrothers")
  2. Salmonella fimH and fimA (Warning: runs for a couple of hours, because MCMC was mixing poorly, so the number of iterations was bumped to 51 M):
    	  demo("salmonella_example", package="rbrothers")
For a list of demos available in the package, type
If you want to copy and modify one of the demo R scripts, you can use the system.file() command to find the location of the script in your tree directory:
	  system.file("demo", "fimH_example.R", package="rbrothers")

R package: robustDist

R package: synDss

Developers: Peter Chi, Vladimir Minin

Contact: Peter Chi,

Overview: R package synDss allows for detection of rare recombination events in molecular sequences. The method implemented in the synDss package is based on a previously developed scanning window recombination detection method (Dss). While the original Dss method uses regular molecular sequence distances measured in expected number of substitutions between sequences, our synDss uses generalized synonymous and nonsynonymous distances measuredin expected number of synonymous and nonsynonymous substitutions respectively. This extension allows us to distinguish between recombination and convergent evolution.

Source code (anonymous subversion access):
svn checkout svn://scm.r-forge.r-project.org/svnroot/evolmod/pkg/synDss

  1. The first step is to download and install PAML. The two programs we need from this software package are codeml and evolver.
  2. In R terminal, install dependencies by typing
    >install.packages(c("ape","phangorn", "seqinr"))
    >install.packages("robustDist", repos="http://R-Forge.R-project.org")
    (see robustDist for more info on installation of this package)
  3. In R terminal, type
     install.packages("synDss", repos="http://R-Forge.R-project.org")
  4. Attention Mac OS X users: R-forge (temporarily?) stopped providing binaries for Mac OS X, so the previous step won't work for you. Instead, download this source file to your Desktop and type in R terminal:
     >install.packages("~/Desktop/synDss.tar", repos = NULL, type="source")

R package: phyloRcppExamples

Developers: Vladimir Minin

Contact: Vladimir Minin,

Overview: R package phyloRcppExamples illustrates how to implement some calculations required for phylogenetic inference using a combination of R and C++ code, using Rcpp package. Currently, the only useful example is a phylogenetic likelihood calculator.

Source code (anonymous subversion access):
svn checkout svn://scm.r-forge.r-project.org/svnroot/evolmod/pkg/phyloRcppExamples
Last modified: August, 2013