recipe braker2

BRAKER2 is an extension of BRAKER1



Other / Artistic License




doi: 10.1093/nargab/lqaa108

BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

package braker2

(downloads) docker_braker2



depends augustus:


depends bamtools:


depends biopython:

depends blast:


depends cdbtools:


depends diamond:


depends exonerate:


depends gemoma:


depends genomethreader:


depends makehub:

depends perl:

depends perl-app-cpanminus:

depends perl-class-data-inheritable:

depends perl-exception-class:

depends perl-file-homedir:

depends perl-file-spec:

depends perl-file-which:

depends perl-hash-merge:

depends perl-list-moreutils:

depends perl-list-util:

depends perl-logger-simple:

depends perl-math-utils:

depends perl-mce:

depends perl-module-load-conditional:

depends perl-parallel-forkmanager:

depends perl-posix:

depends perl-scalar-util-numeric:

depends perl-test-pod:

depends perl-yaml:

depends python:


depends samtools:


depends spaln:




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 braker2

and update with::

   mamba update braker2

To create a new environment, run:

mamba create --name myenvname braker2

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 `braker2/tags`_ for valid values for ``<tag>``)


  • GeneMark software can be used for free, but requires a license file and should be additionally installed on the machine where the BRAKER2 environment is.

  • ProtHint software can be used for free, but doesn't allow redistribution and should be additionally installed on the machine where the BRAKER2 environment is.

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