- RNAhairpinMLsample computes the partition function and samples structures for user-specified number H of hairpins and M of multiloops.
- RNAmultiloop computes the partition function for either number or for order of multiloops.
- ffthairpinZM1 uses FFT to compute the partition function for the number of hairpins.
- fftmultinumZM1 uses FFT to compute the partition function for the number of multiloops.