RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints

CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data

RNA Interaction Format (RIF) with reference implementations in C++, JavaScript, and Python

Official code of RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment.

LaRA 2: Lagrangian Relaxed structural Alignment

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.

RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding

Visualising RNA-RNA interactions

MFE method for predicting the psuedoknotted secondary structures of RNA sequences.

Bioinformatics Data Structures & Algorithms [such as the Q-Gram Index, scoring alignments , rna-structure prediction, generating the BLAST-Ńeighborhood and more.]

Motif-based aligned RNA searcher

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.