TABLE 1.

RNA folding programs based on free energy minimization

Name	Functionsa	URL
mfold	Folding of single and interacting nucleic acids	http://www.bioinfo.rpi.edu/applications/mfold
RNAstructure	Window software for RNA folding and oligo design	http://rna.urmc.rochester.edu/rnastructure.html
Vienna RNA package	Optimal and complete suboptimal folding	http://www.tbi.univie.ac.at/~ivo/RNA
RNAshapes	Abstract shape representation of Vienna suboptimal foldings	http://bibiserv.techfak.uni-bielefeld.de/rnashapes
pknotsRG	Folding including a class of simple pseudoknots	http://bibiserv.techfak.uni-bielefeld.de/pknotsrg
PKNOTS	Folding including a class of pseudoknots	http://selab.wustl.edu/cgi-bin/selab.pl?mode=software
RNALOSS	Locally optimal folding	http://clavius.bc.edu/~clotelab/RNALOSS

^aOnly directly relevant functions are listed.