A SAT
encoding for the Graph Isomorphism problem is described in the SAT 2013 paper "On the Resolution Complexity of Graph non-Isomorphism".
Minisat is one of the best-known SAT solvers, but it has several successors which are probably faster and have a higher success rate. Try Cryptominisat (version 2.9.5 seems to be faster than version 3; it supports parallel threads), Riss3g or Clasp.