Pseudoknot
- PKNOTS 1.07 – RNA Pseudoknot Prediction
- HotKnots 2.0 – Predict Secondary Structures of RNA with or without Pseudoknots
- PSTAG 2.1.4a – Model Pseudoknot RNA Structure
- IPknot 0.0.2 – RNA Secondary Structure Prediction including Pseudoknots
- PseudoViewer 3.0 – Visualization of RNA Pseudoknots of any type
- RNATOPS 1.2 – RNA Pseudoknot Search in Genomes
- Knotted2Nested – Remove Pseudoknots from RNA
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