Now you can breed any bee and mutate any bee. The next step is to create your own designer Queen out of DNA and Protein. You need to craft the Protein Liquifier and the DNA extractor. The Protein Liquefier requires Beef (or any raw meat) and the DNA extractor uses extra bees that you have. The DNA Extractor will also need Genetic Labware in order to produce DNA.
Once these are full, their liquids will need to be pumped into the Genetic Replicator.