TABLE 2.

RNA folding programs for characterizing Boltzmann ensemble of RNA secondary structures, using comprehensive Turner free energy parameters

Name	Functionsa	URL
Sfold	Statistical sampling and clustering, and rational design of nucleic acids	http://sfold.wadsworth.org; http://www.bioinfo.rpi.edu/applications/sfold
RNAstructure	Partition function and base-pair probabilities	http://rna.urmc.rochester.edu/rnastructure.html
Vienna RNA package	Partition function and base-pair probabilities	http://www.tbi.univie.ac.at/~ivo/RNA
NUPACK	Partition function and base-pair probabilities including a class of pseudoknots	http://www.acm.caltech.edu/~niles/software.html

^aOnly directly relevant functions are listed.