## RNAstructure Installation and Overview
Repository Organization

- ### Contents

- ### Index

### Code Directories

Directory | Description
--- | ---
RNA_class | A group of related object wrappers that encapsulate most back end code for easy use
src | Location of most back end code

### GUI Directories

Directory | Description
--- | ---
RNAstructure_java_interface | Cross-platform Java interface capable of running on Linux, Macintosh, or Windows operating systems
RNAstructure_windows_interface | GUI writen natively (using MFC) for Windows operating systems

### Text Interface Directories

Directory | Description
--- | ---
AllSub | Generate a group of suboptimal structures
bifold | Bimolecular folding
bipartition | Bimolecular partition function for predicting pair probabilities
CircleCompare | Compare two structures for the same sequence, with the nucleic acid backbone arranged around a circle to facilitate easy comparisons
ct2dot | Convert CT structure notation to dot bracket structure notation
dot2ct | Convert dot bracket structure notation to CT structure notation
DotPlots | Creates three separate interfaces that can make different dot plot types
draw | Generate Postscript images of secondary structures
DuplexFold | Bimolecular folding without intramolecular pairs
dynalign | Predict the lowest free energy structure common to two sequences
efn2 | Predict folding free energy change of a given structure
EnsembleEnergy | Predict the energy of a structure ensemble.
fold | Single sequence secondary structure prediction by free energy minimization
MaxExpect | Secondary structure prediction by maximizing expected accuracy
multilign | Predict the lowest free energy structure common to more than two sequences
napss | Use NMR data to improve the prediction of an RNA secondary structure
oligoscreen | Screen a set of oligonuceotides for hybridization stability and self-structure
oligowalk | Calculate thermodynamic features of sense-antisense hybridization and predict free energy changes of oligo binding to target RNA
PARTS | Predict pair probabilities for folding of two sequences to a common structure
pfunction | Partition function calculation of base pairing probabilities
ProbablePair | Generate structures composed of only highly probable pairs as determined by a threshold
ProbKnot | Predict pseudoknots for a single sequence
refold | Refold a previously folded structure
RemovePseudoknots | Remove pseudoknots from a structure
RNAstructure_windows_text_interfaces | Text interfaces specifically for Windows
scorer | Calculate sensitivity and positive predictive value for two structures being compared
stochastic | Stochastic sampling from the Boltzman ensemble
TurboFold | Predict the lowest free energy structure common to more than two sequences, using base pairing probabilities.

### Resource Directories

Directory | Description
--- | ---
data_tables | Location of thermodynamic parameters
exe | Holds executables for text interfaces, GUIs, and any libraries
tests | Project tests for each text interface

### Help Directories

Directory | Description
--- | ---
examples | Sample input files
manual | Help and some usage documentation

### Essential Top-Level Files

File Name | Description
--- | ---
compiler.h | Compiler and compilation flags, macros, and definitions
gpl.txt | The GPL license under which the RNAstructure software package falls
library_defines.h | Names for the libraries the repository builds, defined by operating system
Makefile | The main Makefile which builds most of the repository modules
Version.txt | Contains the most recent version number and release date for the repository