:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'sonicparanoid' .. highlight: bash sonicparanoid ============= .. conda:recipe:: sonicparanoid :replaces_section_title: :noindex: SonicParanoid\: fast\, easy and accurate orthology inference :homepage: http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/ :license: GPL3 / GNU General Public License v3 :recipe: /`sonicparanoid `_/`meta.yaml `_ :links: doi: :doi:`10.1093/bioinformatics/bty631` .. conda:package:: sonicparanoid |downloads_sonicparanoid| |docker_sonicparanoid| :versions: .. raw:: html
1.3.8-31.3.8-21.3.8-11.3.8-01.3.7-01.3.6-11.3.6-01.0.14-41.0.14-3 ``1.3.8-3``,  ``1.3.8-2``,  ``1.3.8-1``,  ``1.3.8-0``,  ``1.3.7-0``,  ``1.3.6-1``,  ``1.3.6-0``,  ``1.0.14-4``,  ``1.0.14-3``,  ``1.0.14-2``,  ``1.0.14-1``,  ``1.0.14-0``,  ``1.0.13-0`` .. raw:: html
:depends biopython: ``>=1.79`` :depends blast: ``>=2.12.0`` :depends diamond: ``>=2.0.12`` :depends filetype: ``>=1.0.7`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends mcl: ``>=14.137`` :depends mmseqs2: ``>=13.45111`` :depends numpy: ``>=1.21`` :depends pandas: ``>=1.3.2`` :depends psutil: ``>=5.8.0`` :depends python: ``>=3.8,<3.9.0a0`` :depends python_abi: ``3.8.* *_cp38`` :depends scikit-learn: ``>=0.24.2`` :depends scipy: ``>=1.7.1`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 sonicparanoid and update with:: mamba update sonicparanoid To create a new environment, run:: mamba create --name myenvname sonicparanoid 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/sonicparanoid: (see `sonicparanoid/tags`_ for valid values for ````) .. |downloads_sonicparanoid| image:: https://img.shields.io/conda/dn/bioconda/sonicparanoid.svg?style=flat :target: https://anaconda.org/bioconda/sonicparanoid :alt: (downloads) .. |docker_sonicparanoid| image:: https://quay.io/repository/biocontainers/sonicparanoid/status :target: https://quay.io/repository/biocontainers/sonicparanoid .. _`sonicparanoid/tags`: https://quay.io/repository/biocontainers/sonicparanoid?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sonicparanoid/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/sonicparanoid/README.html