recipe orthofinder

Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!

Homepage:

https://github.com/davidemms/OrthoFinder

License:

GPLv3

Recipe:

/orthofinder/meta.yaml

package orthofinder

versions:

3.0.1b1-0,  2.5.5-2,  2.5.5-1,  2.5.5-0,  2.5.4-0,  2.5.3-0,  2.5.2-1,  2.5.2-0,  2.5.1-0, 

3.0.1b1-0,  2.5.5-2,  2.5.5-1,  2.5.5-0,  2.5.4-0,  2.5.3-0,  2.5.2-1,  2.5.2-0,  2.5.1-0,  2.4.1-1,  2.4.1-0,  2.4.0-1,  2.4.0-0,  2.3.12-0,  2.3.11-1,  2.3.11-0,  2.3.10-0,  2.3.8-2,  2.3.8-1,  2.3.8-0,  2.3.3-1,  2.3.3-0,  2.2.7-0,  2.2.6-0,  2.2.1-0,  2.2.0-0,  2.1.2-1,  2.1.2-0,  1.1.10-0,  1.1.8-0,  1.1.4-0,  1.1.2-0

depends aster:

depends biopython:

depends blast:

depends bzip2:

depends diamond:

<2.1|>=2.1.7

depends fastme:

depends fasttree:

depends iqtree:

depends mafft:

depends mcl:

depends mmseqs2:

depends muscle:

<5

depends python:

>=3.7,<3.12

depends raxml:

depends raxml-ng:

depends scikit-learn:

depends scipy:

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 orthofinder

and update with::

   mamba update orthofinder

To create a new environment, run:

mamba create --name myenvname orthofinder

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/orthofinder:<tag>

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

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