Package viennarna-dev-1.8.5-205

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. The package allows you to - predict minimum free energy secondary structures - calculate the partition function for the ensemble of structures - calculate suboptimal structures in a given energy range - predict consensus secondary structures from a multiple sequence alignment - predict melting curves - search for sequences folding into a given structure - compare two secondary structures - The package includes a Perl5 module that gives access to almost all functions of the C library from Perl. - The following executables are provided in /sw/bin: 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 RNAalifold -- predict the consensus structure of several aligned sequences RNALfold -- predict locally stable structure of long sequences RNAplfold -- compute average pair probabilities for local base pairs RNApaln -- fast structural alignment of RNA sequences using string alignments Kinfold -- explores the folding kinetics of RNA RNAforester -- computes tree-alignments of RNA structures Several small but helpful Perl Utilities are in /sw/share/ViennaRNA/bin which is not added to your PATH by default. -- For more detailed information on these please enter the command info RNA .