Is it possible to run the GETHOGs algorithm on already computed pairs of orthologs from OMA?

Question

[Juan Cordero]

Dear community,

I've downloaded all pairs of orthologs (oma-pairs.txt file) from the OMA website and I wonder whether it is possible to find, for different taxonomic ranges, the HOGs starting from this file, without running the oma standalone program again for all organisms present in the oma-pairs.txt file.

For instance, I would like to find all HOGs in metazoa and then all HOGs in mammals. Would I need to start from scratch and create a DB folder with all metazoa genomes and another DB folder with all mammal genomes, and run oma for every one?

In other words: is it possible to run GETHOGs independently from the OMA standalone program? If yes, which kind of input should I use?

Thanks a lot in advance

Answer 1

[Christophe Dessimoz]

If you don't want to run OMA standalone, you can download all HOGs from the current OMA release—the file ("Hierarchical Orthologous Groups") is linked from this page: http://omabrowser.org/oma/current/

To parse this file and retrieve HOGs defined at the various levels, I recommend that you use this tool:

https://github.com/DessimozLab/familyanalyzer

If you'd like to run the GETHOGs algorithm—perhaps changing some of the default parameters—the easiest way to do this is by exporting precomputed genomes from here and run OMA Standalone (should be very quick)

http://omabrowser.org/oma/export/