OMA analysis with around 400 proteomes

[algiraudg]

Dear Sir/Madam,

Thank you for providing this perfect tool. I am using OMA to infer HOGs for >400 proteomes. After the database checking step and the All Vs All step (working perfectly) were performed, the next step (the orthology calling) take a huge quantity of time (more than 1 month)...
Do you have any issue to decrease the time of computation of this last step? I'd also appreciate any advice about how to modify the parameters.

Thanks,
Alex

[sinamajidian]

Hi Alex
Thanks for contacting us. Could you please tell us your goal of running OmaStandalone? whether you are looking for orthologous pairs, marker genes, or HOGs. Depending on your application you could uncomment some of these lines in the parameter file.

WriteOutput_HOGFasta := false;
WriteOutput_Paralogs := false; 
WriteOutput_PhyleticProfileHOG := false;
WriteOutput_PhyleticProfileOG := false;

Even with that, we agree that it is difficult to run OmaStandalone for hundreds of species (specially eukaryotes). To address this, we recently developed FastOMA which can handle thousands of species. It is available on github here. The preprint is also here.

Best regards,
Sina