RNAmutants: Computation of RNA superoptimal secondary structure and boltzmann partition function of RNA mutants. The software can be downloaded at http://RNAmutants.csail.mit.edu. A web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/.
partiFold: Boltzmann partition function, inter-strand residue contact probability and sampling of transmembrane β-barrel proteins. Updates transFold. A web server is available at http://partiFold.csail.mit.edu/partiFold/.
RNAsat:
Boltzmann partition function and sampling of saturated RNA secondary structure.
transFold: Prediction of the structure and residue contacts of transmembrane proteins. transFold has been updated with partiFold. The old web server is still available at http://theory.csail.mit.edu/transFold/
amsag2c: automatic generation of the C code of the AMSAG algorithm.