ViennaRNA

The ViennaRNA Package is a comprehensive suite of software tools designed to analyze and predict RNA secondary structures. It has been a widely used resource in the field for nearly two decades, offering a range of functionalities based on accurately measured thermodynamic parameters and advanced dynamic programming algorithms. Key features of the ViennaRNA Package include:

Computation of Ground States: Accurately determines the most stable RNA secondary structures.
Base Pairing Probabilities: Calculates the probabilities of base pair formation, aiding in the prediction of RNA behavior.
Thermodynamic Properties: Provides detailed thermodynamic data related to RNA folding.
RNA-RNA Interaction Tools: Expanded repertoire to analyze interactions between different RNA molecules.
Structure Ensembles: Allows for the assessment of restricted ensembles of RNA structures.
Output Information: Generates additional outputs such as centroid structures, maximum expected accuracy structures, and z-scores for locally stable secondary structures.
Input Support: Accepts input in FASTA format, enhancing usability.
Concurrent Computations: Utilizes OpenMP for efficient multi-core processing.
Compatibility: Ensures backward compatibility with earlier versions of the package.