Can FastOMA infer orthologs between distantly related species?

[Yolanda1201]

Hi developers,

Thank you for maintaining FastOMA — it’s a great tool!

I’m currently working on a comparative genomics project involving distantly related plant species. I tried using OrthoFinder, but it failed to recover 1:1 orthologs for many genes across the species I included. In contrast, I read that OMA may be more suitable for distant evolutionary comparisons.

So, I have the following questions:
1. Can FastOMA reliably infer orthologs between distantly related species, where sequence divergence is high (e.g., different orders or families)?
2. Are there any specific parameter settings or recommended input formats to improve sensitivity in such cases?

Any advice or clarification would be greatly appreciated. Thanks again for your work!

Best,
Jingchen Yuan

[sinamajidian]

Hi Jingchen,

Thanks for reaching out and sorry for the late response. In the QfO benchmarks, FastOMA shows good accuracy for distant species at the LUCA level.

We could tweak a few parameters specific to the size of the dataset but the default setting should work well.

Please let us know if you have any other questions.

Best,
Sina