RPHAST: Phylogenetic Analysis with Space/Time Models... in R

Introduction

RPHAST is an R interface to the phast software package. It contains much of the functionality of phast within a highly-developed statistical programming environment, and is easy and fun to use.

Download

Package source: rphast_1.6.tar.gz
Windows binary:rphast_1.6.zip
Development version:rphast_1.6.tar.gz
Latest Windows build (devel):rphast_1.6.zip

Install

RPHAST should install like any R package. It can be obtained and installed via CRAN from within R using the command:
> install.packages("rphast")

Note that if you are running Windows or Mac OS X, you will need an up-to-date version of R for this command to work. On Mac OS X with xcode, you can install onto an older R version with the command:
> install.packages("rphast", type="source")

Or to use the package files provided on this page, use one of these (depending on your platform):
> install.packages("rphast_1.6.tar.gz", repos=NULL) #(to install from source code)
> install.packages("rphast_1.6.zip", repos=NULL) #(to install windows binary)

The package source can also be installed from the command line on non-Windows platforms using the command:
R CMD INSTALL rphast_1.6.tar.gz

NOTE: If you do not have administrator privileges, you may need to specify a directory where the package will be stored. This can be done with the "library" argument to install.packages, or by using R CMD INSTALL --library=/path/to/library on the command line.

Documentation

PDFSweave sourcedescription
vignette1.pdfvignette1.RnwRead in alignment and features, estimate neutral model based on 4d sites using phyloFit, run phyloP and phastCons
vignette2.pdfvignette2.RnwDetect rodent-accelerated regions using a multiple species alignment of human chromosome 22, assess significance by simulation
vignette3.pdfvignette3.RnwCreate custom phylogenetic HMM which models a transcription factor binding site; verify the model on a simulated alignment
vignette4.pdfvignette4.RnwIntroduction to detecting GC-biased gene conversion with RPHAST; nucleotide and phylo-HMM models
rphast-manual.pdf Reference manual

Publications

Hubisz MJ, Pollard KS, and Siepel A. PHAST and RPHAST: Phylogenetic Analysis with Space/Time Models. (in press, Briefings in Bioinformatics).


Plans

We are continuously adding functionality to RPHAST, and eventually hope it will encompass most of phast's features. We are prioritizing development based on need, so let us know if particular features would be helpful!


Contact

Problems, questions, feature requests should be directed to phasthelp@cshl.edu.