recipe r-rphast

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.

Homepage:

http://compgen.cshl.edu/rphast

License:

BSD / BSD_3_clause + file LICENSE

Recipe:

/r-rphast/meta.yaml

package r-rphast

(downloads) docker_r-rphast

versions:
1.6.11-0,  1.6.9-9,  1.6.9-8,  1.6.9-7,  1.6.9-6,  1.6.9-5,  1.6.9-4,  1.6.9-3,  1.6.9-2, 

1.6.11-0,  1.6.9-9,  1.6.9-8,  1.6.9-7,  1.6.9-6,  1.6.9-5,  1.6.9-4,  1.6.9-3,  1.6.9-2,  1.6.9-1,  1.6.9-0

depends blis:

>=0.9.0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends pcre:

>=8.45,<9.0a0

depends r-base:

>=4.5,<4.6.0a0

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-rphast

and update with::

   mamba update r-rphast

To create a new environment, run:

mamba create --name myenvname r-rphast

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-rphast:<tag>

(see `r-rphast/tags`_ for valid values for ``<tag>``)

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Link to this page

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