One thing i would find very useful and maybe other users as well is, when you select a clade, to be able to mask the segments which are shared between all the taxa in that clade. Probably not removing them directly when zooming but giving the option of hiding them.
This would help a lot in exploring other recombination segments affecting part of the selected taxa, specially in very recombining organisms where Gubbins output is very dense...
Just a suggestion!
One thing i would find very useful and maybe other users as well is, when you select a clade, to be able to mask the segments which are shared between all the taxa in that clade. Probably not removing them directly when zooming but giving the option of hiding them. This would help a lot in exploring other recombination segments affecting part of the selected taxa, specially in very recombining organisms where Gubbins output is very dense... Just a suggestion!