That doesn't really say us what you want..
Completely automated with Pure Bees is Easy, and there is no reason to Analyze them. Wood Pipe on Bottom/Top, Stone/Cobble Pipe, Apiarist Pipe on the side. Say the Apiarist Pipe send Bees back into the Apiary. Items Somewhere and "Anything" somewhere else. (Anything includes Bees and Items, but only when there is no other way for them)
When you want a Half automatic Breeding Station for Mutating. Just do the same but without putting them back in the Apiary and let them go into an Analyzer (Needs liquid honey from a Squeezer). And from the Analyzer to some Chest.
Don't do Mutating Automatic, that will screw everything up.