I've used Blast2GO in the past but now I'm thinking about switching to open-source tools.
My current idea is get the GO terms database via InterPro and then perform the enrichment with R, possibly topGO. However, my experience with topGO in the past in not the best, compared to Blast2GO. I was missing quite a lot of significant GO terms!
The species is a non-model fungus.
Maybe guys you have a better alternative for my purpose, at least for the enrichment step. Thanks!