recipe blosum

A small module for easy access to BLOSUM matrices without dependencies.



GPL3 / GPL-3.0-or-later



The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics. Reading such matrices is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies. And why do we need to implement the same reader again if there is a simple module for that. blosum offers a robust and easy-to-expand implementation without relying on third-party libraries.

package blosum

(downloads) docker_blosum



depends python:




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 blosum

and update with::

   mamba update blosum

To create a new environment, run:

mamba create --name myenvname blosum

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

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