| Name | Description | |
|---|---|---|
| Tertiary structure databases | ||
| NDB | the nucleic acid database | |
| SCOR | a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships. | |
| Alignment and consensus secondary structure databases | ||
| CRW Site | alignments, structure models and phylogenetic analyses of 5S, 16S and 23S rRNA, Group I and II introns and tRNA. | |
| Rfam | a large collection of multiple sequence alignments and covariance models covering common non-coding RNA families. | |
| Ribosomal Database Project-II | The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community. | |
| RiboWeb | RiboWeb is composed of the serveral integrated RNA information resources. | |
| RNA FRABASE | RNA FRAgments search engine and dataBASE. | |
| Silva | A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data. | |
| SRPDB | the Signal Recognition Particle Database contains aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. | |
| The tmRNA Website Research | a collection of tmRNA sequences, alignments, secondary structures and other information. | |
| tmRDB | tmRDB (tmRNA Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of tmRNA. | |
| The RNase P Database | a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. | |
| Viral RNA Structure Database | Viral structures from TBI. | |
| General sequence alignment methods | ||
| BLAST | The Basic Local Alignment Search Tool (BLAST) compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. | |
| CLUSTALW | a general purpose multiple sequence alignment program. | |
| FASTA | a searcher for local alignments against proteins and nucleotides databases. | |
| MUSCLE | MUltiple Sequence Comparison by Log-Expectation. | |
| T-COFFEE | a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, protein sequences and structures. | |
| RNA alignment methods by 2D structural information | ||
| LGSFAligner | a Local Gapped Subforest Aligner for pairs of RNA secondary structures. | |
| LocARNA | LocARNA is a tool for multiple alignment of RNA molecules. | |
| MiGaL | a program for comparing RNA secondary structures and building phylogenetic trees. | |
| RNA_align | aligns two RNA structures using an edit distance model. | |
| RNAdistance | a program for calculating measures for secondary structure dissimilarity. | |
| RNAforester | a program for comparing and aligning RNA secondary structures via the "forest alignment" approach. | |
| RNAshapes | a program that uses the "consensus shapes" method to predict an abstract shape common to RNA sequences. | |
| Alignment methods for RNA 2D structures with pseudoknots | ||
| PSTAG | a pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures. | |
| RNA searching methods by sequence/structural information | ||
| ERPIN | an RNA motif search program. | |
| HomoStRscan | a program for discovering homologous RNAs in complete genomes. | |
| Infernal | a program to construct a RNA profile based upon an alignment and consensus structure. | |
| RADAR | a web-based server for RNA data analysis and research. | |
| RaveNnA | a software package for fast covariance modeling of RNA sequences. | |
| RNACAD | a stochastic context-free grammar (SCFG) RNA modeling package. | |
| RNAmotif | a program for searching a database for RNA sequences that match a "motif" of secondary structure interactions. | |
| RSEARCH | a program for aligning an RNA query to target sequences, using SCFG algorithms. | |
| Palingol | a descriptive programming language to describe nucleic acid's secondary structure and scan sequence databases. | |
| PHMMTS | an implementation of pair hidden Markov models on tree structures. | |
| RNA phylogenetic analysis tools | ||
| CBCanalyzer | a program for inferring phylogenies based on compensatory base changes. | |
| jRNA | a program for exploring insect (and other less interesting) phylogenies using RNA secondary structure. | |
| MrBayes | a program for the Bayesian estimation of phylogeny. | |
| PHASE | a program designed for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. | |
| RRNADIST, RRNAML and RNAML | a program for modeling empirical substitutions for Ribosomal RNA. | |
| SISSI | a software tool for generating data of related sequences along a given phylogeny. | |
| RNA folding software | ||
| Afold | a program for analyzing internal loops within RNA secondary structures. | |
| alteRNA | alteRNA is an alternative to many RNA folding methods. | |
| CONTRAfold | a secondary structure prediction method based on conditional log-linear models (CLLMs). | |
| inteRNA | inteRNA predicts the joint secondary structure of two RNA sequences. | |
| Kinfold | a program to simulate the stochastic folding kinetics of RNA sequences into secondary structures. | |
| MC-FOLD/MC-Sym | The MC-Fold | MC-Sym pipeline is a web-hosted service for RNA secondary and tertiary structure prediction. | |
| RNAfold | an MFE RNA structure prediction algorithm. | |
| RNA Kinetics | a program to simulate the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. | |
| RNAstructure | a Windows implementation of the Zuker algorithm for RNA secondary structure prediction based on free energy minimization. | |
| Sfold | a statistical sampling of all possible RNA secondary structures. | |
| UnaFold (MFold) | an MFE RNA structure prediction algorithm. | |
| Vsfold4 | a program that folds single RNA sequences using an extended energy model. | |
| RNA single sequence 2D prediction with pseudoknots | ||
| HotKnots | a heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. | |
| Hpknotter | a heuristic approach for detecting RNA H-type pseudoknots. | |
| KineFold | a folding kinetics program of RNA sequences including pseudoknots. | |
| McQFold | a program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence. | |
| NUPACK | a dynamic programming algorithm based on the partition function for the prediction of a restricted class of RNA pseudoknots. | |
| Pknots-RG | a dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. | |
| Pknots | a dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. | |
| Algorithm for 2D with suboptimal predictions | ||
| Barriers | a program to compute local minima and energy barriers of the RNA folding landscape. | |
| RNALOSS | a program for local and optimal secondary structure computation. | |
| RNAshapes | a program to select unique suboptimal structures (shapes) based on an abstract representation of RNA secondary structure. | |
| RNAsubopt | a program to calculate all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). | |
| Algorithm for 2D with suboptimal predictions with pseudoknots | ||
| MPGAfold | A massively parallel genetic algorithm for predicting RNA secondary structures with pseudoknots. | |
| RNA 2D prediction by alignments | ||
| BayesFold | a program to find, rank, and draw the likeliest structures for a sequence alignment. | |
| ConStruct | a tool for thermodynamic controlled prediction of conserved secondary structure. | |
| Garna | a program for predicting secondary structures of RNAs using a genetic algorithm. | |
| Genebee | a RNA alignment folding program that uses a combination of free-energy and mutual information. | |
| Pfold | a program for folding alignments using a SCFG trained on rRNA alignments. | |
| RNAalifold | a program for folding alignments using a combination of free-energy and a co-variation measures. | |
| RNAlishapes | a tool for RNA structure analysis based on aligned RNA sequences. | |
| RNAGA | a program for predicting common RNA secondary structures using a genetic algorithm. | |
| RNA 2D prediction by alignments with pseudoknots | ||
| Circles | an experimental Windows 95/98/NT program for inferring RNA secondary structure using a comparative method. | |
| HXMATCH | a program for computing a consensus structure including pseudoknots based on an alignment of a few RNA sequences. | |
| ILM | an iterated loop matching program that evaluates stems in an alignment using a combination of free-energy and mutual information. | |
| KnetFold | a program that computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning approaches. | |
| Mifold | a matlab package for investigating mutual information content of RNA alignments. | |
| Simultaneous alignment and structure prediction methods | ||
| CaRNAc | a program for comparative analysis combined with MFE folding. | |
| Cmfinder | an RNA motif prediction tool. | |
| Consan | a program to produce pairwise RNA secondary structural alignments. | |
| COVE | an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. | |
| Dynalign | a "full energy model" and comparative information to align and fold 2 two RNA sequences. | |
| Foldalign | a program that predicts conserved local sequence and hair-pin structures using CONSENSUS and CLUSTAL-like heuristics. | |
| LARA | a program that produces a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation. | |
| RNAcast | a RNA consensus abstract shapes technique for multiple RNA folding. | |
| RNAmine | is a software tool for extracting the structural motifs from a set of RNA sequences. | |
| SEED | a program that uses suffix arrays to enumerate complementary regions, possibly containing interior loops, as well for matching RNA secondary structure expressions. | |
| Stemloc | a comparative RNA-structure finder that uses accelerated pairwise stochastic context-free grammars. | |
| Simultaneous alignment and structure prediction methods with pseudoknots | ||
| comRNA | a program for predicting common RNA secondary structure motifs in a group of related sequences. | |
| RNA Tertiary structural tools | ||
| AMIGOS/PRIMOS/Qnifft | a series of tools for working with RNA/DNA structure files. | |
| Assemble | a graphical tool to construct and study RNA structures. | |
| ARTS | Alignment of RNA Tertiary Structures based on quadrats RNA representation. | |
| BERNACLE | a Python library for RNA 3D structure prediction. | |
| ERNA-3D | a program to create and manipulate RNA 3D coordinates. | |
| FARNA/FARFAR | a program for predicting RNA 3D structure using the Web version of the Rosetta server | |
| FR3D | a program for finding small RNA motifs (two to 20 nucleotides) in PDB files | |
| iFoldRNA | a web portal for interactive RNA folding simulations. | |
| MC-Sym | a software that builds RNA 3-D structures using coordinates and relations between residues extracted from X-ray crystallography and NMR. | |
| MANIP | a program that allows the rapid assembly of separate motifs into a complex three-dimensional architecture. | |
| ModeRNA | a program for comparative RNA modeling. | |
| NAB | a program to construct models for non-helical nucleic acids. | |
| NASSAM | a program that searches for motifs and formations of nucleic acid bases in 3D space within nucleic acid PDB formatted structures. | |
| NAST | a Nucleic Acid Simulation Tool. | |
| Ribostral | an RNA 3D alignment analyzer and viewer based on basepair isostericities. | |
| RNA2D3D | a program that can generate, view and compare RNA 3D structures available in the package StructureLab | |
| RNABuilder/MMB | a tool for building 3D RNA models using a variety of knowledge the user has about the structure. | |
| RNAComposer | a user-friendly program to the fully automated prediction of large RNA 3D structures. | |
| RNA-MolIP | an integer programming framework that refines predicted secondary structures. | |
| ROSETTA | The Rosetta Commons aims to develop high resolution protein/RNA prediction and design software. | |
| S2S | a program to display, manipulate and interconnect RNA sequence and strucure data. | |
| VFold | software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures.s. | |
| YUP | a package for molecular simulations of reduced representation models. | |