Dear OMA team!
I like your program, since there are very few tools that help to find “true”-orthologs, and your papers convinced me OMA
is one of them.
I have several questions to you.
1) I don’t like to run OMA on our cluster, it takes a lot of time, uses many nodes and my colleagues do not approve it. It turned out now it is possible to run it locally – I need to find orthologs to several proteins only. It works but BLAST finds more protein hits… Some of them are not “true”-orthologs, but many are.
2) What is your default database? I found some proteins have not been there yet. I need to run OMA in many bacteria for a single protein, or even in all finished bacterial genomes for a single protein. Is it possible right now with OMA ?
3) What would be your advice -what script should I use to make OMA run as fast as possible? Our cluster is rather specific – scripts suggested in your papers do not work on it.
4) What is the latest update – I have not found any articles published later than in 2015. How can I update my old OMA version?
5) Where can I find a detailed description of the current OMA algorithm?
Thank you very much indeed! Sincerely yours, Natalia