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RNAstructure Installation and Overview
Interfaces Summary

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/java_interface
Description: A cross-platform GUI for RNAstructure.
To Build: In the 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?