recipe bcftools-snvphyl-plugin

The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection\ of microbial genomes and constructing a phylogenetic tree. This package is the bcftools C plugin



Apache / Apache-2.0



package bcftools-snvphyl-plugin

(downloads) docker_bcftools-snvphyl-plugin



depends bcftools:


depends bzip2:


depends curl:


depends libgcc-ng:


depends libzlib:


depends openssl:


depends xz:


depends zlib:




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 bcftools-snvphyl-plugin

and update with::

   mamba update bcftools-snvphyl-plugin

To create a new environment, run:

mamba create --name myenvname bcftools-snvphyl-plugin

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<tag>

(see `bcftools-snvphyl-plugin/tags`_ for valid values for ``<tag>``)

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