recipe biodiff

exact comparison of biological sequences






biodiff is a variant caller that determines the exact differences between two biological sequences. It can operate on DNA and protein sequences, as long as they are in fasta format. The sequences to be compared must have the same fasta header (up to the first whitespace). If the reference and query each have only one sequence, however, the header need not match and the comparison will be done, but a warning will be emitted. Output is in the Variant Call Format.

package biodiff

(downloads) docker_biodiff



depends libgcc-ng:


depends perl:



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 biodiff

and update with::

   mamba update biodiff

To create a new environment, run:

mamba create --name myenvname biodiff

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 `biodiff/tags`_ for valid values for ``<tag>``)

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