[zellyn]

Do I understand correctly that this kind of constraint satisfaction is more complex than just turning things into a bunch of SAT clauses? Otherwise (and admittedly without a deep understanding of genomics or solvers), I would be surprised if constraint satisfaction were the best approach for edit distance…

Once you added domain-specific performance-oriented constraints, did you find this to be a useful and viable approach to the problem?

[sirwhinesalot]

MiniZinc is just a modeling language, you can throw the problem at different solvers. You can use SAT solvers (assuming you have some wrapper that translates FlatZinc to CNF), CP solvers (can be SAT-based underneath or use different algorithms like MAC), SMT solvers (SAT Modulo Theories like Arithmetic), MIP solvers (usually Simplex + Branch & Bound)...