recipe count_constant_sites

Compute the count of cases in constant sites in a (FASTA) multiple sequence alignment

Homepage:

https://github.com/pvanheus/count_constant_sites

License:

MIT

Recipe:

/count_constant_sites/meta.yaml

Given a FASTA file with a multiple sequence alignment of nucleotides, this tool counts the sites in the alignment that are constant. The output is a line suitable for use in IQTREE's `-fconst`, thus 4 numbers with commas expressing the count of As, Cs, Gs and Ts.

package count_constant_sites

(downloads) docker_count_constant_sites

versions:

0.1.1-1,  0.1.1-0

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 count_constant_sites

and update with::

   mamba update count_constant_sites

To create a new environment, run:

mamba create --name myenvname count_constant_sites

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/count_constant_sites:<tag>

(see `count_constant_sites/tags`_ for valid values for ``<tag>``)

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