Hi, I'm new to homology and OMA. In my project, I would like to generate the whole genome homology between different individuals of the same species. I have assembled 3 different individuals genome, and also generated their annotation. Now I ran OMA standalone to estimate the homology between these individuals together with several sister species downloaded from OMA database. I found that the resulted file 'OrthologousGroups.txt ' for OMA group is very useful, and it's what I would like to have, despite that it's lacking the paralogy information.

So my goal is to get a homology group gene list from HOG information. I have checked the OMA primer instruction and pyham instruction , and I still didn't figure out how I can generate a list of genes of HOG. Meanwhile, I checked the HOGFasta folder in the output of OMA, and notice that each HOG has its own fast file that includes all the homologous genes.

So my questions are : (1) Can I just simply list all the gene names in each HOG fasta file to get the homology gene list? If I understand correctly of OMA, paralogs has their own HOG number, right? (2) If the (1) gets a NO, then how shall I generate the homology gene list? Could you give me some hints here?

Thanks a lot!