ViennaRNA (DISABLED - will be removed on 8/10/2017)

NOTE: Due to lack of use, the ViennaRNA software module has been disabled and will be removed from MSI systems on 8/10/2017. If you need this software, please contact




The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

To load this software in a Linux environment run the commands:
module load viennarna
Now, type the name of the desired stand-alone program from the list below

Additional Information

For a detailed information, take a look at the HTML versions of the man pages for the programs at

  • RNAfold -- predict minimum energy secondary structures and pair probabilities
  • RNAeval -- evaluate energy of RNA secondary structures
  • RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
  • RNAinverse -- inverse fold (design) sequences with predefined structure
  • RNAdistance -- compare secondary structures
  • RNApdist -- compare base pair probabilities
  • RNAsubopt -- complete suboptimal folding
  • RNAplot -- RNA structure drawings in PostScript, SVG, or GML
  • RNAcofold -- predict hybrid structure of two sequences
  • RNAduplex -- predict possible hybridization sites between two sequences
  • RNAup -- predict RNA-RNA interaction sites using accessibilities
  • RNAalifold -- predict the consensus structure of several aligned sequences
  • RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
  • RNALfold -- predict locally stable structure of long sequences
  • RNAplfold -- compute average pair probabilities for local base pairs in long sequences
  • RNApaln -- fast structural alignment of RNA sequences using string alignments
  • Several small but helpful Perl Utilities


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