Take a multiple whole genome alignment (MAF or fasta) and associated genome annotations (GFF) and generate a ortholog/paralog map. To keep it simple, overlapping annotations would qualify as paralog/ortholog if they cover each other reasonably well in the WGA (e.g. 75% sequence overlap).
Mugsy-annotator would work for bacterial genomes but not for larger Eukaryota (at least not for the data that I have).
Is there an elegant solution already around or is that something I would need to develop by myself?
Ideas are very much appreciated.