How do I simulate Golden Gate assembly in SnapGene?
SnapGene versions 6.0.x and earlier do not have a dedicated tool for simulation of Golden Gate Assembly.
You can use Actions → Restriction Cloning → Insert Multiple Fragments to simulate Golden Gate Assembly of a vector and fragments with appropriate Type IIS enzyme sites (e.g. BsaI).
For more information see the lesson Insert Multiple Restriction Fragments into a Plasmid.
SnapGene 6.1 and later has a dedicated Golden Gate tool. See the Golden Gate Assembly chapter to learn how to perform simulation of Golden Gate assembly in SnapGene 6.1 and later.