RNAstructure Command Line Help: Index

RNAstructure Command Line Help
Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A AccessFold: Overview AccessFold: References AccessFold: Run Information Alignment File Format alignments AllSub: Overview AllSub: References AllSub: Run Information	N NAPSS: Overview NAPSS: References NAPSS: Run Information NMR Data Integrated With Structure Prediction
B bifold: Overview bifold: References bifold: Run Information Bimolecular Folding Bimolecular Duplex Folding Bimolecular Duplex Folding with Accessibility Bimolecular Partition Function bipartition: Overview bipartition: References bipartition: Run Information Building the Text Interfaces	O Offset File Format oligoscreen: Overview oligoscreen: References oligoscreen: Run Information OligoWalk
C Calculating Ensemble Energy Calculating Common Structures For Multiple Sequences Calculating Common Structures For Two Sequences CircleCompare: Overview CircleCompare: References CircleCompare: Run Information Comparing Two Structures Converting Bracket Files to CT Files Converting CT Files to Bracket Files CT File Format ct2dot: Overview ct2dot: References ct2dot: Run Information cuda: partition-cuda	P partition: Overview partition: References partition: Run Information Partition Function Single Strand PARTS: Overview PARTS: References PARTS: Run Information pathways for analysis phmm Probability of Pairs in Two Unaligned Sequences ProbabilityPlot: Overview ProbabilityPlot: References ProbabilityPlot: Run Information ProbablePair: Overview ProbablePair: References ProbablePair: Run Information ProbKnot: Overview ProbKnot: References ProbKnot: Run Information ProbScan Pseudoknot Prediction: ProbKnot Pseudoknot Prediction: ShapeKnots
D dot2ct: Overview dot2ct: References dot2ct: Run Information draw: Overview draw: References draw: Run Information Drawing Secondary Structures Drawing a Base Pairing Probability Dot Plot Drawing a Dynalign Dot Plot Drawing a Folding Free Energy Dot Plot DuplexFold: Overview DuplexFold: References DuplexFold: Run Information dynalign: Overview dynalign: References dynalign: Run Information dynalign-smp: Overview dynalign-smp: References dynalign-smp: Run Information DynalignDotPlot: Overview DynalignDotPlot: References DynalignDotPlot: Run Information	Q
E efn2: Overview efn2: References efn2: Run Information Energy Function 2 EnergyPlot: Overview EnergyPlot: References EnergyPlot: Run Information EnsembleEnergy: Overview EnsembleEnergy: References EnsembleEnergy: Run Information Experimental Pair Bonus File Format	R refold: Overview refold: References refold: Run Information Refolding Previously Folded Structures RemovePseudoknots: Overview RemovePseudoknots: References RemovePseudoknots: Run Information Removing Pseudoknots
F FASTA File Format File Formats Folding Free Energy Calculation Fold: Overview Fold: References Fold: Run Information Fold-cuda Folding Constraint File Format Folding Single Stranded Structures Folding on GPUs	S scorer: Overview scorer: References scorer: Run Information Scoring a Structure's Quality Sequence File Format SHAPE Restraint File Format ShapeKnots Specifying Thermodynamic Parameters Stochastic Sampling
G Generating All Suboptimal Structures Generating Probable Structures	T Thermodynamic Parameters for Oligos TurboFold: Overview TurboFold: References TurboFold: Run Information
H	U
I Identifying Pseudoknots Information flow	V
J	W
K	X
L List File Format	Y
M MaxExpect: Overview MaxExpect: References MaxExpect: Run Information Maximum Expected Accuracy Structures Multifind: Overview Multifind: Run Information multilign: Overview multilign: References multilign: Run Information multilign-smp: Overview multilign-smp: References multilign-smp: Run Information	Z