evolmod: R packages for evolutionary modeling

Available R packages:

rbrothers - detects recombination using a Bayesian multiple change-point model
robustDist - estimates labeled evolutionary distances (e.g. synonymous and nonsynonymous distances)
synDss - detects recombination using synonymous and/or nonsynonymous distances
phyloRcppExamples - playground for Rcpp applied to phylogenetic algorithms

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.

E. coli fimH (runs for about 2 minutes):

	  demo("fimH_example", package="rbrothers")

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

	  demo(package="rbrothers")

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")

References:

Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN. rbrothers: R package for Bayesian multiple change-point recombination detection, Evolutionary Bioinformatics, 9, 235-238, 2013.
Minin VN, Dorman KS, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection, Bioinformatics, 21:3034-3042, 2005.
Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS. Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model, Journal of the American Statistical Association 98:427-437, 2003.
Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS. Oh brother, where art thou? a Bayes factor test for recombination with uncertain heritage, Systematic Biology 51:715-728, 2002.

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

Installation:

The first step is to download and install PAML. The two programs we need from this software package are codeml and evolver.
- For codeml, the included MS Windows executable (codeml.exe) will work as is on Windows, and on Linux/Mac, one can compile codeml.c following the PAML installation instructions.
- For evolver, we need to compile it in a slightly different way in order to allow for variable dN/dS rates at each site (i.e. the M3 model). Essentially, we need to go to the PAML subdirectory that contains evolver.c, and type:
```
gcc -O4 -DCodonNSsites -o evolverNSsites evolver.c tools.c -lm
```
  This is assuming that a gcc compiler is installed on your machine, e.g. through RTools if you are using Windows. See this README file for more details.
- Put the binary files codeml and evolverNSsites into your environmental variable PATH or if you don't know how to do this, just record the full directory path to these file, so you can pass this information to synDss functions.

In R terminal, install dependencies by typing

>install.packages(c("ape","phangorn", "seqinr"))

and

>install.packages("robustDist", repos="http://R-Forge.R-project.org")

(see robustDist for more info on installation of this package)

In R terminal, type

 install.packages("synDss", repos="http://R-Forge.R-project.org")

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")
```

References:

Chi P, Chattopadhyay S, Sokurenko EV, Minin VN. Untangling Convergent Evolution and Recombination, to be posted on arxiv soon, 2013.
McGuire G, Wright F, Prentice MJ. A graphical method for detecting recombination in phylogenetic data sets, Molecular Biology and Evolution, 14:1125-1131, 1997.
O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences, Molecular Biology and Evolution, 26:801-814, 2009.

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