RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and the latest nearest neighbor parameters from the Turner group. The software includes methods for predicting secondary structures, base pair probabilities, bimolecular structure prediction, and structures common to two sequences. New extensions include a C++ class library for integration into other programs, a user-friendly Java GUI, and Unix-style text interfaces. The software is available for download from the Mathews lab homepage. RNAstructure is designed to make RNA secondary structure prediction accessible to a wide range of users. It offers user-friendly GUIs for Windows, Linux/Unix, and Mac OS-X, as well as text interfaces for command-line use and scripting. A C++ class library allows developers to incorporate RNAstructure functions into new programs. The package is available under the GNU Public License, version 2. The software includes a C++ class library that encapsulates RNAstructure's I/O functions and secondary structure prediction methods. Four main classes are provided: RNA for single sequence predictions, Dynalign_object for Dynalign calculations, HybridRNA for bimolecular structure prediction, and Oligowalk_object for OligoWalk and OligoScreen calculations. The classes are designed for easy integration into C++ projects and are compiled into shared libraries for various platforms. The text interfaces provide RNAstructure's features for command-line and script use. They include online help and are available for Windows, Linux, and macOS. The RNAstructure class library is used to implement most of the text interface functions, making them useful for tutorials. The new Java GUI is a cross-platform reimplementation of the Windows GUI, designed to be user-friendly. It uses the RNAstructure C++ class library and is accessible via SWIG. The Java GUI is available for macOS and Linux. RNAstructure includes various algorithms for single-sequence and multi-sequence structure prediction. It uses thermodynamic parameters to predict RNA and DNA secondary structures, incorporating experimental data for improved accuracy. The software also includes unit testing for algorithm validation. RNAstructure is available for download and is compatible with multiple operating systems. It requires C++ for the class library and Java for the GUI. The software is licensed under the GNU Public License and is freely available for non-academic use.RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and the latest nearest neighbor parameters from the Turner group. The software includes methods for predicting secondary structures, base pair probabilities, bimolecular structure prediction, and structures common to two sequences. New extensions include a C++ class library for integration into other programs, a user-friendly Java GUI, and Unix-style text interfaces. The software is available for download from the Mathews lab homepage. RNAstructure is designed to make RNA secondary structure prediction accessible to a wide range of users. It offers user-friendly GUIs for Windows, Linux/Unix, and Mac OS-X, as well as text interfaces for command-line use and scripting. A C++ class library allows developers to incorporate RNAstructure functions into new programs. The package is available under the GNU Public License, version 2. The software includes a C++ class library that encapsulates RNAstructure's I/O functions and secondary structure prediction methods. Four main classes are provided: RNA for single sequence predictions, Dynalign_object for Dynalign calculations, HybridRNA for bimolecular structure prediction, and Oligowalk_object for OligoWalk and OligoScreen calculations. The classes are designed for easy integration into C++ projects and are compiled into shared libraries for various platforms. The text interfaces provide RNAstructure's features for command-line and script use. They include online help and are available for Windows, Linux, and macOS. The RNAstructure class library is used to implement most of the text interface functions, making them useful for tutorials. The new Java GUI is a cross-platform reimplementation of the Windows GUI, designed to be user-friendly. It uses the RNAstructure C++ class library and is accessible via SWIG. The Java GUI is available for macOS and Linux. RNAstructure includes various algorithms for single-sequence and multi-sequence structure prediction. It uses thermodynamic parameters to predict RNA and DNA secondary structures, incorporating experimental data for improved accuracy. The software also includes unit testing for algorithm validation. RNAstructure is available for download and is compatible with multiple operating systems. It requires C++ for the class library and Java for the GUI. The software is licensed under the GNU Public License and is freely available for non-academic use.