rphast : Interface to PHAST Software for Comparative Genomics

Copyright: All code is Copyright (c) 2002-2016 University of
California, Cornell University, Cold Spring Harbor Laboratory.
Package: rphast
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
License: BSD_3_clause + file LICENSE
Title: Interface to PHAST Software for Comparative Genomics
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Description: Provides 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: 1.6.4
URL: http://compgen.cshl.edu/rphast
Date: 2016-05-25
Imports: methods
Depends: stats
Suggests: ape, seqLogo
Collate: 'bgc.R' 'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R'
'optim.R' 'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R'
'rphast.R' 'treeModel.R' 'trees.R' 'zzz.R'
RoxygenNote: 5.0.1
Packaged: 2016-06-01 18:50:26 UTC; rramani
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-06-02 05:58:21