R interface to PHAST software for comparative genomics
'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R'
'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R' 'rphast.R'
'treeModel.R' 'trees.R'

'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'

RPHAST is an R interface to the PHAST package
(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.

All code is Copyright (c) 2002-2016 University of
California, Cornell University, Cold Spring Harbor Laboratory.
Interface to PHAST Software for Comparative Genomics
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.

All code is Copyright (c) 2002-2018 University of
California, Cornell University, Cold Spring Harbor Laboratory.
Interface to 'PHAST' Software for Comparative Genomics
Provides an R interface to the 'PHAST'(<http://compgen.cshl.edu/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.