Question on providing custom annotations

[GabrieleRigano99]

Hi! First of all I'd like to thank you for your work, I was really looking for a tool like this one.
My question is: can I provide in any way some custom annotations? I am working on fungi belonging to the Sporothrix genus, I have already annotated them with other softwares using RNAseq data. Since I have 12 annotations of different strains of the same species I wanted to use them as evidence. Is there a way to do this? Thank you!

[YanNevers]

Dear @GabrieleRigano99 ,

I apologize for the big delay. My notifications for this repository were not set correctly and I missed this question...
I would understand if you have already moved on but I will answer nonetheless.

It is possible to provide custom annotation to be part of the homology information to use to inform the consensus.

So in this case:
If you have different potential annotations for one of your sample (the target), you can include them on a single branch of a the input tree. Then include all the existing annotations you have for the other strain as direct outgroups of the target. For using OMA, you can just provide the protein FASTA files of these species in the DB folder at the same time as the target files.

Note that if you are looking to do a consensus for annotation of the different strains, it might not be possible directly using OMAnnotator as it assume the consensus will be done over a single genome. However, there might be alternative to do so using the OMA framework.

If you are still interested, feel free to let me know if I did not answer fully. You can also contact me directly via email to work out a solution.

Best wishes,
Yannis Nevers