I'd like to see a list of the restriction enzymes that don't cut my DNA (so I can clone these sites in myself). As far as I can see, this isn't currently possible in Ugene and unfortunately I have to keep using Bioedit to do this instead.

Thanks, that is what I was after - to find a group of enzymes that don't cut the sequence. I don't often use the circular view, which is why I hadn't spotted it before.

I guess a more minor suggestion, then, would be whether the enzymes that don't cut could be included in the linear view. When I select 'Actions-Analyze-Find restriction sites' there's an option for minimum hits, which can be set to zero, although enzymes with zero hits don't show up in the linear results. I'd also like to be able to save the list of enzymes to compare with hits from another sequence, i.e. find a list of enzymes that cut neither sequence.