I have whole genome seq data from a non-model organism (Bengalese finch - Lonchura striatta domestica), which I've mapped and annotated using another organism for which there's more info available (Zebra finch https://uswest.ensembl.org/Taeniopygia_guttata/Info/Index and https://www.ncbi.nlm.nih.gov/assembly/GCA_003957565.1/) . as in KEGG https://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=tgu and also supported by PANTHER if I use a customized ref list and use a list of IDs from Reference Proteome Genome http://pantherdb.org/tools/uploadRefFile.jsp.

I did some popgen/evo analysis and have couple lists of genes of interests, which I would like to check for functional enrichment.

What would be the optimal way of doing this?