OMA Standalone - orthology inference pipeline among custom and public genomes

The OMA (Orthologous MAtrix) database <https://omabrowser.org>_ is a leading resource for identifying orthologs, that are homologous genes started diverging through a speciation event, among publicly available complete genomes. Orthologs are essential for many applications in molecular biology, including gene function prediction or species tree reconstruction.

OMA standalone is a standalone package that can infer orthologs with the OMA algorithm for custom genomes. It is possible to export genomes <https://omabrowser.org/export>_ and their homology relations directly from the OMA web-browser and combine them with custom genomes or proteomes.

Documentation

The documentation of OMA standalone is available from here <https://omabrowser.org/standalone>_.

Installation

We provide compiled and packaged versions of OMA standalone <https://omabrowser.org/standalone>_ on the OMA Browser website for Linux and MacOSX. OMA does not run on Windows.

You can also install OMA standalone via Homebrew <https://brew.sh/> or Linuxbrew <http://linuxbrew.sh/>:

.. code-block:: bash

brew tap brewsci/bio
brew install oma

Docker ++++++

OMA standalone is also available from on Docker. You simply need to bind mount the folder with your dataset into the docker's /oma path. So the command to run the ToyExample dataset within this repository would be:

.. code-block:: bash

docker run --rm --name oma -v "$(pwd)/ToyExample:/oma" \ dessimozlab/oma_standalone:latest oma

Running from source +++++++++++++++++++

If you want to use OMA standalone from this repository, make sure you have Darwin <http://bio-recipes.com/darwin/>_ installed on your system.