We design flexible fault tolerant gate gadgets that allow the data and the ancilla to be encoded using different codes. By picking a stabilizer code for the ancilla we are able to perform both Clifford and non-Clifford gates fault tolerantly on generic quantum codes, including both stabilizer and non-additive codes. This allows us to demonstrate the first universal fault tolerant gate set for non-additive codes. We consider fault tolerance both with respect to a dephasing channel and a depolarizing channel.