rphast

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.

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Description file content

Copyright
All code is Copyright (c) 2002-2018 University of California, Cornell University, Cold Spring Harbor Laboratory.
Package
rphast
Maintainer
Ritika Ramani
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
1.6.9
URL
Date
2018-01-30
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
2018-01-30 15:54:53 UTC; rramani
NeedsCompilation
yes
Repository
CRAN
Date/Publication
2018-02-11 15:39:12 UTC

install.packages('rphast')

1.6.9

6 months ago

http://compgen.cshl.edu/rphast

Ritika Ramani

BSD_3_clause + file LICENSE

Depends on

stats

Imports

methods

Suggests

ape, seqLogo

Discussions