The OMA (Orthologous MAtrix) database 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 and their homology relations directly from the OMA web-browser and combine them with custom genomes or proteomes.
The documentation of OMA standalone is available from here.
We provide compiled and packaged versions of OMA standalone on the OMA Browser website for Linux and MacOSX. OMA does not run on Windows.
You can also install OMA standalone via Homebrew or Linuxbrew:
brew tap brewsci/bio
brew install omaOMA 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:
docker run --rm --name oma -v "$(pwd)/ToyExample:/oma" \
dessimozlab/oma_standalone:latest omaIf you want to use OMA standalone from this repository, make sure you have Darwin installed on your system.