rphast: Interface to PHAST Software for Comparative Genomics

RPHAST is an R interface to the PHAST software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.

Version: 1.6
Depends: stats
Suggests: ape, seqLogo
Published: 2015-01-14
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Maintainer: Melissa Hubisz <mjhubisz at cornell.edu>
License: BSD_3_clause + file LICENSE
Copyright: All code is Copyright (c) 2002-2015 University of California, Cornell University.
URL: http://compgen.cshl.edu/rphast
NeedsCompilation: yes
Materials: ChangeLog
In views: Phylogenetics
CRAN checks: rphast results


Reference manual: rphast.pdf
Vignettes: RPHAST intro, phyloFit, phyloP, phastCons
Custom phylo-HMM with RPHAST
GC-biased gene conversio
Package source: rphast_1.6.tar.gz
Windows binaries: r-devel: rphast_1.6.zip, r-release: rphast_1.6.zip, r-oldrel: rphast_1.6.zip
OS X Mavericks binaries: r-release: rphast_1.6.tgz, r-oldrel: rphast_1.6.tgz
Old sources: rphast archive

Reverse dependencies:

Reverse imports: rtfbs