improving synteny visualization for polyploid

[Levi Bauer]

Hi everyone,

I've been having a lot of success with Circos, thanks for developing such a robust program for visualization. My current issue is synteny and the ribbons drawn between coordinates. My one species is a hexaploid plant with 36 chromosomes in the haploid genome and so there's a boatload of syntenic regions. It looks like a rainbow swirl currently. I've tried running mcscanx with decreasing (more stringent) evalue cutoffs, but even then that part of the plot is still incredibly busy.

Do you have any advice for settings I could change/ways I could improve this issue?