RNA
- CorreLogo 1.2.6 – 3D Sequence Logos of RNA and DNA Alignments
- LocARNA 1.7.6 – Global and Local Alignment of RNA
- RCAT 3.0 – RNA Comparative Analysis Tools
- ncFANs v2 – non-coding RNA Function Annotation Server
- Ribostral 20070223 – RNA Sequence Alignment Analysis program
- FR3D 20120611 – Find Structural Motifs in RNA 3D Structures
- r-make 1.0b – Process RNA Sequencing Reads
- RNAstructure 5.5 – Prediction & Analysis of RNA Secondary Structure
- Circles 0.1.1 – Analysis of RNA Secondary Structure
- RNAclust 1.3 – Cluster RNAs based on Secondary Ctructures
- Vienna RNA Package 2.1.1 – RNA Secondary Structure Prediction & Comparison
- NanoTiler 0.11.1 – Design of RNA Nanostructures
- RNA2D3D 5.7.0 – Conversion of RNA 2D Structures to 3D and 3D Modeling
- KNetFold 1.4.4b – RNA secondary structure prediction
- MPGAfold / MPGAfold Visualizer – Massively Parallel Genetic Algorithm that Predicts RNA Secondary Structure
- StructureLab 4.5.0 – RNA Structure Analysis
- Evolving SCFGs 2.0 – RNA Secondary Structure Prediction
- tantan 13 – Find Cryptic Repeats in DNA, RNA, and Protein Sequences.
- CURE 1.1 – Cytidine-to-Uridine RNA Editing Predictor
- eteRNA – RNA Game Lets Players Help Find a Biological Prize
- DNA/RNA/Protein and General Molecular Weight Calculator 1.0
- Starfold – Predict RNA Secondary Structures
- RNAbor – Compute Structural Neighbors of an RNA Secondary Structure
- rnaifold – RNA Inverse Folding and Molecular Design
- DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection
- VARNA 3-9 – Java pplet for Drawing the Secondary Structure of RNA
- Assemble2 1.0 beta1 – Construct & Study RNA Architectures
- rNA 1.0 / mrNA 1.0 / grNA 0.9 – randomized Numerical Aligner
- RNA draw 1.1b2 – RNA Secondary Structure Calculation & Analysis
- loopDloop 2.07b – Draw RNA Secondary Structures
- RLooM – RNA Loop Modeling
- ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence
- RNAAnalyzer – Identify Regulatory RNA Elements
- GTfold 3.0 – Scalable Multicore Code for RNA Secondary Structure Prediction
- RNABOB 2.2 – Fast Pattern Searching for RNA Secondary Structures
- SStructView 1.2.2 – RNA Secondary Structure Viewing Java Applet
- Context Fold 1.0 – RNA Secondary Structure Prediction tool
- FRUUT 2.40 – Fast RNA Unrooted Unordered Tree Alignment
- RNAMute – RNA Secondary Structure Mutation Analysis Tool
- ILM 20030728 – Predict RNA Secondary Structures with Pseudoknots
- SSPcompare – Takes a Library of known RNA Sequence-structure Pairs
- RNAwolf 0.3.2 / MC-Fold-DP – RNA Secondary Structure Prediction.
- CMCompare 0.0.1 – Discriminatory Power of RNA Family Models
- barriers 1.5.2 – Basin Structure of RNA Energy Landscapes
- expected5to3distance – Compute Expected Distance between Terminal Nucleotides of RNA
- Dishuffle – RNA Dinucleotide Shuffle
- BlastR 2.2 – Searching and Clustering RNA
- ModeRNA 1.7.1 – Comparative RNA 3D Modeling
- RALEE 0.7 – RNA ALignment Editor in Emacs
- RNAmotifs 3 – Predict a motif for your own set of RNAs
- WEAV 0.2 – de novo Assembly program for both Genome and RNA
- RNAmutants 1.1.0 – Exploring the Effects of Mutations on the Secondary Structure of RNAs
- RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering
- ESSA – Analyse RNA Secondary Structure
- PKNOTS 1.07 – RNA Pseudoknot Prediction
- CONSAN 1.2 – Pairwise Structural RNA Alignment
- Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test
- RADAR 2.0 – RNA Data Analysis and Research
- Erpin 5.5.4 – RNA Motif Search program
- ARTS – Alignment of RNA Tertiary Structures
- MEMERIS 1.0 – MEME in Rna’s Including Secondary Structures
- MARNA 100729 – Server for Multiple Alignment of RNAs
- LocalFold 1.0 – Local Folding of RNA
- INFO-RNA 2.1.2 – A Server for Inverse Folding of RNA
- RNAplex 0.2 – Search for Short Interactions between two long RNAs
- HelixPSO – Particle Swarm Optimizer for RNA Secondary Structure Prediction
- FOLDALIGN 2.1.1 / FOLDALIGNM 1.0.1 – RNA Structure and Sequence Alignment
- SARSE 1.37 – RNA Sequence Editor
- ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool
- HotKnots 2.0 – Predict Secondary Structures of RNA with or without Pseudoknots
- MultiRNAFold 2.0 – Secondary Structure Prediction of RNA/DNA
- Rchange – Compute Energy Changes of RNA Secondary Structures
- Rentropy – Compute Entropy of RNA Secondary Structures
- Kinefold – RNA/DNA Folding Predictions
- jViz.Rna 2.0 – Visual Comparison of RNA Secondary Structure
- SeqLogo – Create Sequence Logo from RNA alignment file
- RNA – RNA Consensus Secondary Structure Prediction Software
- IPknot 0.0.2 – RNA Secondary Structure Prediction including Pseudoknots
- CONTRAfold 2.02 – RNA Secondary Structure Prediction
- DNASIS MAX 3.0 – Bioinformatics Software for DNA/RNA/Amino Acid Sequence Analysis
- HALO 1.3 – Precise RNA de novo Transcript Half-life Determination
- RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure
- PseudoViewer 3.0 – Visualization of RNA Pseudoknots of any type
- RNAv – Search Genomes for RNA Secondary Structure Variation
- RNATOPS 1.2 – RNA Pseudoknot Search in Genomes
- RNApasta 1.01 – RNA Structural Alignment & Statistical Analysis
- RNAfamily – Java Viewer for RNA Secondary Structures
- Rnall 2.0 – RNA Local Secondary Structure Prediction
- XRNA 1.2.0b – Creation, Annotation & Display of RNA Secondary Structure Diagrams
- RNAsifter 1.0 – RNA Shape Index Filter
- RNAhybrid 2.1 – Find Minimum Free Energy Hybridisation of RNA
- RNAMovies 2.0.4 – Visualization of RNA Secondary Structure
- GUUGle 1.2 – Fast Exact Matching under RNA Base Pairing Rules
- RnamlView 1.0 – Manipulation, Storage & Visualisation of RNA Data
- RNAView – Generates 2-dimensional Displays of RNA/DNA Secondary Structures
- RNAmmer 1.2 – Ribosomal RNA Sub Units
- Knotted2Nested – Remove Pseudoknots from RNA
- RNAMotif 3.0.7 – Find Structural Motifs in RNA
- comRNA 1.80 – Common RNA Secondary Structure Predictor
- Suitename 0.3 – RNA Conformer
- RNABC 1.11 – RNA Backbone Correction
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