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: | 1.6.5 |
| Depends: | stats |
| Imports: | methods |
| Suggests: | ape, seqLogo |
| Published: | 2016-08-16 |
| 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) 2002-2016 University of California, Cornell University, Cold Spring Harbor Laboratory. |
| 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_1.6.5.tar.gz |
| Windows binaries: | r-devel: rphast_1.6.5.zip, r-release: rphast_1.6.5.zip, r-oldrel: rphast_1.6.5.zip |
| OS X Mavericks binaries: | r-release: rphast_1.6.5.tgz, r-oldrel: rphast_1.6.5.tgz |
| Old sources: | rphast archive |
| Reverse imports: | rtfbs |
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