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.

Hi! I am not sure if I get it right. Do you want to find all enzymes, which do not cut the sequence or do you want to know if some specific enzymes do not cut the sequence? In the latter case you can just select  a group of enzymes and then use Restriction Sites Map from Circular View in order to see which restriction sites are not present. (see screenshot attached)

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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.