Infrared
A generic framework for tree-decomposition powered sampling and optimization based on declarative models. Allows to implement diverse optimization and Boltzmann sampling tasks, e.g. in design, network phylogeny, and structure alignment, that can be expressed as constraint satisfaction problems with additional evaluations. Provides automatic generic solving with efficiency depending on the tree width (more intuitively, depending on the complexity of dependencies in the problem instance).
VARNA
Drawing and editing the RNA secondary structure in publication-ready quality. Accepts a wide range of documented and illustrated options. It offers rich user interaction through a graphical user interface. For automation, it is accessible via a Python API.
LocARNA
Fast simultaneous folding and alignment of RNAs. Provides several tools for structure-based comparison of multiple RNAs (of potentially unknown structure), which integrate practically relevant features like structure and sequence anchor constraints. High efficiency due to exploiting sparsity on structure and sequence levels.
IPANEMAP
IPANEMAP predicts RNA secondary structures compatible with multiple structure probing (SHAPE, DMS, Enzymatic…) data, potentially under different conditions (ions, temperature…). IPANEMAP Suite uses this software as integral part of a comprehensive modelling pipeline that guides practitioners from direct analysis of SHAPE data to multi-profile structure modelling and differential analysis.
LiCoRNA
Structure sequence alignment for two RNAs in the presence of arbitrary pseudoknots. The program is based on the tree decomposition of query sequence and a general parameterized algorithm to compute the optimal alignment.
RNARedPrint
Design of RNAs with multiple conformations. Uses an FPT dynamic programming scheme to sample sequences under expressive constraints to solve the positive design of RNA. Reimplemented as RNARedPrint 2.0 in Infrared.