recipe macse

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.

Homepage:

https://bioweb.supagro.inra.fr/macse/

License:

CeCILL 2.1

Recipe:

/macse/meta.yaml

Links:

biotools: macse, doi: 10.1093/molbev/msy159

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence

package macse

versions:

2.07-0,  1.2-1,  1.2-0

depends openjdk:

>=1.5

requirements:

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 macse

and update with::

   mamba update macse

To create a new environment, run:

mamba create --name myenvname macse

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/macse:<tag>

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

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