I am a Gene Ontology newbie. I have a Maker annotated GFF3 file for a non-model organism. I want to experiment with term enrichment analyses for genes in regions of the genome under positive selection. I believe the first step is generating some GO IDs from the evidence I have (blastx, blastn, genome2protein, ect...)? I have looked at blast2go, but I don't want to use software that is not free / open source.
I would also really appreciate any advice on how to be conservative in these analyses. I am often skeptical of GO enrichment analyses, but don't know what the quality metrics are.