recipe pipelign

A pipeline for automated multiple sequence alignment, particularly of viral sequences.






package pipelign

(downloads) docker_pipelign



depends biopython:

depends cd-hit:

depends ete3:

depends hmmer:

depends iqtree:

depends joblib:

depends mafft:

depends parallel:

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 pipelign

and update with::

   mamba update pipelign

To create a new environment, run:

mamba create --name myenvname pipelign

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

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