recipe bioconductor-msa2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MSA2dist.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-msa2dist/meta.yaml

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.

package bioconductor-msa2dist

versions:

1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-pwalign:

>=1.2.0,<1.3.0

depends bioconductor-pwalign:

>=1.2.0,<1.3.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-ape:

depends r-base:

>=4.4,<4.5.0a0

depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-rcpp:

depends r-rcppthread:

depends r-rlang:

depends r-seqinr:

depends r-stringi:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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 bioconductor-msa2dist

and update with::

   mamba update bioconductor-msa2dist

To create a new environment, run:

mamba create --name myenvname bioconductor-msa2dist

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/bioconductor-msa2dist:<tag>

(see `bioconductor-msa2dist/tags`_ for valid values for ``<tag>``)

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