The Program RNAcofold

RNAcofold works much like RNAfold but uses two RNA sequences as input which are then allowed to form a dimer structure. In the input the two RNA sequences should be concatenated using the `&' character as separator. As in RNAfold the -p option can be used to compute partition function and base pairing probabilities.

Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers (see the man page for details).