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/3.16/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 calcualtes pairwise IUPAC distances.

package bioconductor-msa2dist

Versions:

1.2.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-ape

• r-base >=4.2,<4.3.0a0

• r-doparallel

• r-dplyr

• r-foreach

• r-rcpp

• r-rcppthread

• r-rlang

• r-seqinr

• r-stringi

• r-stringr

• r-tibble

• r-tidyr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-msa2dist

and update with:

conda update bioconductor-msa2dist

or 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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Link to this page

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