## RNAstructure Installation and Overview
Interfaces Summary

- ### Contents

- ### Index

Name: | AllSub
Type: | Text Interface
Location: | RNAstructure/AllSub
Description: | Generate a group of suboptimal structures.
To Build: | In the RNAstructure/ directory, type "make AllSub."

Name: | bifold
Type: | Text Interface
Location: | RNAstructure/bifold
Description: | Do bimolecular secondary structure prediction by free energy minimization, allowing intramolecular pairs.
To Build: | In the RNAstructure/ directory, type "make bifold."

Name: | bipartition
Type: | Text Interface
Location: | RNAstructure/bipartition
Description: | Do a bimolecular partition function with two sequences, not allowing intramolecular pairs.
To Build: | In the RNAstructure/ directory, type "make bipartition."

Name: | CircleCompare
Type: | Text Interface
Location: | RNAstructure/CircleCompare
Description: | Compare two structures by creating a postscript file, overlaying their backbones on a circle.
To Build: | In the RNAstructure/ directory, type "make CircleCompare."

Name: | ct2dot
Type: | Text Interface
Location: | RNAstructure/ct2dot
Description: | Convert a CT structure file to a dot bracket structure file.
To Build: | In the RNAstructure/ directory, type "make ct2dot."

Name: | dot2ct
Type: | Text Interface
Location: | RNAstructure/dot2ct
Description: | Convert a dot bracket structure file to a CT structure file.
To Build: | In the RNAstructure/ directory, type "make dot2ct."

Name: | draw
Type: | Text Interface
Location: | RNAstructure/draw
Description: | Draw a Postscript image of a structure.
To Build: | In the RNAstructure/ directory, type "make draw."

Name: | DuplexFold
Type: | Text Interface
Location: | RNAstructure/DuplexFold
Description: | Do bimolecular secondary structure prediction by free energy minimization, with intramolecular pairs forbidden.
To Build: | In the RNAstructure/ directory, type "make DuplexFold."

Name: | dynalign
Type: | Text Interface
Location: | RNAstructure/dynalign
Description: | Find the common secondary structure for two sequences.
To Build: | In the RNAstructure/ directory, type "make dynalign."

Name: | dynalign-smp
Type: | Text Interface
Location: | RNAstructure/dynalign
Description: | Find the common secondary structure for two sequences. This program can be run in a parallel SMP environment.
To Build: | In the RNAstructure/ directory, type "make dynalign-smp."

Name: | DynalignDotPlot
Type: | Text Interface
Location: | RNAstructure/DotPlots
Description: | Create a Postscript dot plot of pairing energies from a Dynalign save file.
To Build: | In the RNAstructure/ directory, type "make DynalignDotPlot."

Name: | efn2
Type: | Text Interface
Location: | RNAstructure/efn2
Description: | Calculate the folding free energy change of structures.
To Build: | In the RNAstructure/ directory, type "make efn2."

Name: | EnergyPlot
Type: | Text Interface
Location: | RNAstructure/DotPlots
Description: | Create a Postscript dot plot of pairing energies from a folding save file.
To Build: | In the RNAstructure/ directory, type "make EnergyPlot."

Name: | EnsembleEnergy
Type: | Text Interface
Location: | RNAstructure/EnsembleEnergy
Description: | Calculate the ensemble folding free energy change for a sequence.
To Build: | In the RNAstructure/ directory, type "make EnsembleEnergy."

Name: | Fold
Type: | Text Interface
Location: | RNAstructure/fold
Description: | Fold a single sequence into its lowest free energy conformation.
To Build: | In the RNAstructure/ directory, type "make Fold."

Name: | Java Cross-Platform Interface
Type: | GUI Interface
Location: | RNAstructure/RNAstructure_java_interface
Description: | A cross-platform GUI for RNAstructure.
To Build: | In the RNAstructure/RNAstructure_java_interface directory, type "make."

Name: | MaxExpect
Type: | Text Interface
Location: | RNAstructure/MaxExpect
Description: | Predict maximum expected accuracy structures.
To Build: | In the RNAstructure/ directory, type "make MaxExpect."

Name: | multilign
Type: | Text Interface
Location: | RNAstructure/multilign
Description: | Find the structures common for more than two homologous sequences.
To Build: | In the RNAstructure/ directory, type "make multilign."

Name: | multilign-smp
Type: | Text Interface
Location: | RNAstructure/multilign
Description: | Find the structures common for more than two homologous sequences. This program can be run in a parallel SMP environment.
To Build: | In the RNAstructure/ directory, type "make multilign-smp."

Name: | NAPSS
Type: | Text Interface
Location: | RNAstructure/napss
Description: | Use NMR data to assist in predicting secondary structure.
To Build: | In the RNAstructure/ directory, type "make NAPSS."

Name: | oligoscreen
Type: | Text Interface
Location: | RNAstructure/oligoscreen
Description: | Calculate thermodynamic properties of a set of oligonucleotides.
To Build: | In the RNAstructure/ directory, type "make oligoscreen."

Name: | OligoWalk
Type: | Text Interface
Location: | RNAstructure/OligoWalk
Description: | Calculate affinity of target RNA binding by oligomers complementary to a specified RNA target.
To Build: | In the RNAstructure/ directory, type "make OligoWalk."

Name: | partition
Type: | Text Interface
Location: | RNAstructure/pfunction
Description: | Calculate the partition function of a sequence.
To Build: | In the RNAstructure/ directory, type "make partition."

Name: | PARTS
Type: | Text Interface
Location: | RNAstructure/PARTS
Description: | Calculate common structures and pairing probabilities for two unaligned sequences.
To Build: | In the RNAstructure/ directory, type "make PARTS."

Name: | ProbabilityPlot
Type: | Text Interface
Location: | RNAstructure/DotPlots
Description: | Create a Postscript dot plot of base pair probabilities from a partition function save file.
To Build: | In the RNAstructure/ directory, type "make ProbabilityPlot."

Name: | ProbablePair
Type: | Text Interface
Location: | RNAstructure/ProbablePair
Description: | Output structures composed of pairs with pairing probabilities that exceed one or more specific probability thresholds.
To Build: | In the RNAstructure/ directory, type "make ProbablePair."

Name: | ProbKnot
Type: | Text Interface
Location: | RNAstructure/ProbKnot
Description: | Predict secndary structures that may contain pseudoknots.
To Build: | In the RNAstructure/ directory, type "make ProbKnot."

Name: | refold
Type: | Text Interface
Location: | RNAstructure/refold
Description: | Refold a previously folded sequence.
To Build: | In the RNAstructure/ directory, type "make refold."

Name: | RemovePseudoknots
Type: | Text Interface
Location: | RNAstructure/RemovePseudoknots
Description: | Remove as few pairs as possible to transform a pseudoknotted structure into a non-pseudoknotted one.
To Build: | In the RNAstructure/ directory, type "make RemovePseudoknots."

Name: | scorer
Type: | Text Interface
Location: | RNAstructure/scorer
Description: | Score a predicted structure against an accepted one.
To Build: | In the RNAstructure/ directory, type "make scorer."

Name: | stochastic
Type: | Text Interface
Location: | RNAstructure/stochastic
Description: | Sample structures from the Boltzmann ensemble.
To Build: | In the RNAstructure/ directory, type "make stochastic."

Name: | TurboFold
Type: | Text Interface
Location: | RNAstructure/TurboFold
Description: | Find the structures common for more than two homologous sequences, using base pairing probabilities.
To Build: | In the RNAstructure/ directory, type "make TurboFold."

Name: | TurboFold-smp
Type: | Text Interface
Location: | RNAstructure/TurboFold
Description: | Find the structures common for more than two homologous sequences, using base pairing probabilities. This program can be run in a parallel SMP environment.
To Build: | In the RNAstructure/ directory, type "make TurboFold-smp."

Name: | Windows Native Interface
Type: | GUI Interface
Location: | RNAstructure/RNAstructure_windows_interface
Description: | A natively compiled Windows GUI for RNAstructure.
To Build: | TODO?

Name: | Windows Text Interfaces
Type: | Text Interface
Location: | RNAstructure/RNAstructure_windows_text_interfaces
Description: | Natively compiled Windows text interfaces for RNAstructure.
To Build: | TODO?