Methods and systems for designing integrated circuits. In one exemplary method, matched registers between the two netlists are determined. The matched registers become cut off points to generate primary inputs and outputs. When there are one or more unmatched registers between the first netlist and the second netlist, the unmatched registers are pushed to the primary inputs or outputs using retiming. At the primary inputs, a subspace generator is used to generate subspaces. The subspaces are used to identify non-equivalences between the first and second netlists. Other features and embodiments are also described.