I have orthologous gene output from OrthAgogue. I want to compare between genera, between clades and within clades. Between clades and between genera can be accomplished using Venn diagrams without too much fuss (I have 2 genera, one with 2 clades, one with 4, a maximum of 17 strains per clade).
I want to find out how to visualise the interactions within clades groups. I've read about UpSet but I'm having a hard time deciding whether it would be appropriate or not, given that all together I have 12512 gene clusters.
Any suggestions would be greatly appreciated!