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RPHAST: Phylogenetic Analysis with Space/Time Models in R

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 and Install

To install the latest version of the package directly from github using the devtools package, use the command in R:

  devtools::install_github("CshlSiepelLab/RPHAST")

The RPHAST package source code can be downloaded here - rphast_1.6.11.tar.gz

RPHAST can be installed from source code using the command in R:

  install.packages("rphast_1.6.11.tar.gz", repos=NULL, type="source")

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

PDF	Sweave Source	Description
Vignette1.pdf	Vignette1.Rnw	Read in alignment and features, estimate neutral model based on 4d sites using phyloFit, run phyloP and phastCons
Vignette2.pdf	Vignette2.Rnw	Detect rodent-accelerated regions using a multiple species alignment of human chromosome 22, assess significance by simulation
Vignette3.pdf	Vignette3.Rnw	Create custom phylogenetic HMM which models a transcription factor binding site; verify the model on a simulated alignment
Vignette4.pdf	Vignette4.Rnw	Introduction to detecting GC-biased gene conversion with RPHAST; nucleotide and phylo-HMM models
RPHAST-Manual.pdf		RPHAST Reference Manual

Publications

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

Contact

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