Using synteny informaiton is slow - how can I improve the performance?
Dear @paulklemm and the developers,
Thanks for developing this excellent tool.
I am running an orthology analysis of about 20 eukaryote species with 20,000-25,000 genes each. It runs fast and efficient on 40 threads if I only depend on DIAMOND, but if I include GFF3 gene coordinates as per the instructions it becomes very slow.
It also seems to gradually slow down over time, suggesting it may take more than a month or so to finish.
Is there something I can do to speed up the orthology inference while including synteny information?
Best regards, Andreas