recipe cyntenator

progressive gene order alignments

Homepage:

https://github.com/dieterich-lab/cyntenator

License:

GPL

Recipe:

/cyntenator/meta.yaml

Cyntenator identifies conserved syntenic blocks between multiple genomes. The program computes Smith-Waterman alignments of sequences, whereby the alphabet consists of all annotated genes and the scoring system is defined by protein sequence similarities and distances between species in a phylogenetic tree. The algorithm is an extension of the Syntenator partial order aligner, described in Rödelsperger and Dieterich, 2008.

package cyntenator

(downloads) docker_cyntenator

versions:

0.0.r2326-3,  0.0.r2326-2,  0.0.r2326-1,  0.0.r2326-0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

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 cyntenator

and update with::

   mamba update cyntenator

To create a new environment, run:

mamba create --name myenvname cyntenator

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/cyntenator:<tag>

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

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