Fully Homomorphic Encryption (FHE) is an active research area with respect to the preservation of privacy, particularly given the recent attention to Post-quantum Cryptography (PQC). It is well known that existing public key crypto systems will be under threat in a quantum computation world, and FHE solutions provide an opportunity to replace existing ‘mathematically hard’ problems with ones that are thought to be quantum safe. FHE libraries have existed for some time, however they are difficult to use and require specialist cryptographic knowledge. To enter the mainstream of software development, suitable compiler technology is needed. Compiler development for FHE is in its infancy and this paper will evaluate two of the most promising solutions that have a potential application to bioinformatics, using suitable metrics to understand how mature or otherwise the leading contenders are.