RNAstructure is a software package designed for predicting and analyzing RNA secondary structures. It utilizes thermodynamics and the latest nearest neighbor parameters from the Turner group to predict the stability of RNA structures. The package includes methods for secondary structure prediction, base pair probability prediction, bimolecular structure prediction, and common structure prediction for multiple sequences. New extensions to RNAstructure include a C++ class library, a user-friendly graphical user interface (GUI) written in JAVA, and new Unix-style text interfaces. The original Windows GUI remains available. The software is available for download from the Mathews lab homepage and is licensed under the GNU Public License, version 2. The package is designed to be user-friendly and accessible, making it suitable for a wide range of applications, including the design of small interfering RNAs and antisense DNA oligonucleotides.RNAstructure is a software package designed for predicting and analyzing RNA secondary structures. It utilizes thermodynamics and the latest nearest neighbor parameters from the Turner group to predict the stability of RNA structures. The package includes methods for secondary structure prediction, base pair probability prediction, bimolecular structure prediction, and common structure prediction for multiple sequences. New extensions to RNAstructure include a C++ class library, a user-friendly graphical user interface (GUI) written in JAVA, and new Unix-style text interfaces. The original Windows GUI remains available. The software is available for download from the Mathews lab homepage and is licensed under the GNU Public License, version 2. The package is designed to be user-friendly and accessible, making it suitable for a wide range of applications, including the design of small interfering RNAs and antisense DNA oligonucleotides.