Vienna RNA package
The Vienna RNA Package consists of a Clibrary and a set of standalone programs to solve problems related to RNA secondary structures. Among them are (sub)optimal structure prediction, RNARNA interaction analysis, energy evaluation, folding path identification, consensus structure prediction, and structural alignment.
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Publications
Fast Folding and Comparison of RNA Secondary Structures
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
In: Monatshefte Chemie, 1994, 125, 167188
doi:10.1007/BF00818163 bibtex 
ViennaRNA Package 2.0
Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
In: Algorithms Mol Biol., 2011, 6, 26
doi:10.1186/17487188626 bibtex 
alidot  Detecting Conserved RNA Structures
alidot is designed to detect conserved RNA secondary structures in small data sets of related RNA sequences. The method is a combination of structure prediction and comparative sequence alignment.
More information is contained in the README file. The program alidot and the associated perl scripts are part of the Vienna RNA Package.
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Publications
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, Peter F. Stadler
In Nucl.Acids Res., 1998, 26, 38253836
doi:10.1093/nar/26.16.3825 bibtex 
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker and Peter F. Stadler
In Comp Chem., 1999, 23, 401414
doi:10.1016/S00978485(99)000133 bibtex 
AREsite  database for the detailed investigation of AUrich elements
AREsite is an online resource for the investigation of AUrich elements (ARE) in vertebrate mRNA UTR sequences hosted at the Institute of Theoretical Chemistry, University of Vienna. AREs are one of the most prominent cisacting regulatory elements found in 3' vertebrate, untranslated regions of mRNAs. Various AREbinding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequencespecific motifs. This online resource allows detailed investigation of these functional elements by analysis of the phylogentic conservation and the structural context these motifs are embedded in. Moreover, AREsite provides information about experimentally validated targets from extensive literature search.
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Publications
AREsite: a database for the comprehensive investigation of AUrich elements
Andreas R Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, Ivo L Hofacker
In Nucleic Acids Research, 2011, 39, Database issue, D66D69
doi:10.1093/nar/gkq990 bibtex 
barriers  Basin Structure of RNA Energy Landscapes
barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For each local minimum found it prints the conformation of the minimum, its energy, the number of the "parent"minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation, basin sizes, etc. can be gathered as well.
The barriers program is fundamental to compute global folding kinetics (using treekin) of RNA molecules.
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Publications
Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L Hofacker, Peter F Stadler, Michael T Wolfinger
In Zeitschrift für Physikalische Chemie, 2002, 216, 2, 155
doi:10.1524/zpch.2002.216.2.155 bibtex 
Efficient computation of RNA folding dynamics
Michael T Wolfinger, W Andreas SvrcekSeiler, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
In Journal of Physics A: Mathematical and General, 2004, 37, 17, 47314741
doi:10.1088/03054470/37/17/005 bibtex 
barMap
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Publications
BarMap: RNA folding on dynamic energy landscapes
Ivo L Hofacker, Christoph Flamm, Christian Heine, Michael T Wolfinger, Gerik Scheuermann, Peter F Stadler
In RNA, 2010, 16, 7, 13081316
doi:10.1261/rna.2093310 bibtex 
Basin hopping graph framework
B(asin)H(opping)G(raph) is a novel coarsegrained model to approximate the folding landscapes of RNA molecules. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when there exists an ``energetically favorable'' direct transition between them. The weights on the edges are the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated efficiently and with high accuracy for RNAs well beyond the length range accessible to enumerative algorithms. The BHG contains more information than the barrier tree. The barrier tree is equivalent to the dendrogram obtained from the BHG by single linkage clustering. Efficient heuristics are utilized to overcome the stringent length restrictions imposed by enumerative approaches. The framework consists of two largely independent components:

The RNAlocmin program generates a sample set of
local minima within a userdefined energy range above the ground
state. This component replaces the exhaustive enumeration of all low energy
states and uses an adaptive schedule for setting up its parameters.
 The BHGbuilder algorithm is then used to estimate
direct saddle points and to determine BHGadjacency on the input set of
LMs. As we show below, the edges and edge weights can be
estimated along the way.
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Bcheck  rnpB gene prediction
Bcheck is a wrapper tool for rnpB gene prediction by combining speed of rnabob descriptor model and sensitivity of infernal covariance model.
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Publications
Bcheck: a wrapper tool for detecting RNase P RNA genes
Dilmurat Yusuf, Manja Marz, Peter F Stadler, Ivo L Hofacker
In BMC Genomics, 2010, 11, 1, 432
doi:10.1186/1471216411432 bibtex 
codaln  Alignments of Nucleic Acid Sequences
codaln produces multiple nucleic acid alignments using information on coding and noncoding regions as part of the scoring function. This is done in order to prevent the problem of higher sequence divergency on the level of nucleic acids as compared to the underlying protein sequences in the case of coding at a certain region of the input nucleic acid sequences.
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Publications
Multiple sequence alignments of partially coding nucleic acid sequences
Roman R Stocsits, Ivo L Hofacker, Claudia Fried, Peter F Stadler
BMC Bioinformatics, 2005, 6(1), 160
doi:10.1186/147121056160 bibtex 
Nucleic Acid Sequence Alignments of Partly Coding Regions
Roman R. Stocsits
Dissertation, 2003, University of Vienna 
CMcompare
The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.
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Publications
cycdeco  Relevant Cycles of undirected graphs
cycdeco reads undirected unweighted graphs (GMLformat) and calculates a minimum cycle bases, the set of relevant cycles, the set of shortest and unique shortest and essential cycles, or the interchangeability classes of relevant cycles.
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Publications
A note On Minimum Path Bases
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
Presented at the conference Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 2427 2001.
Abstract 
Relevant Cycles in Chemical Reaction Network
Petra M. Gleiss, Peter F. Stadler, A. Wagner, and David A. Fell
In Adv. Complex Systems, 2001, 4, 207226
Abstract bibtex 
Graph Grammar Library (GGL)
A rule based chemical reaction application
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Publications
The Graph Grammar Library  a generic framework for chemical graph rewrite systems
Martin Mann, Heinz Ekker, and Christoph Flamm
In Proc. of International Conference on Model Transformation (ICMT) 2013, LNCS, Pages 5253, (2013). ISBN: 9783642388828 (Print) 9783642388835 (Online)
doi:10.1007/9783642388835_5 
Evolution of metabolic networks: a computational framework
Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L Hofacker, Peter F Stadler
In Journal of Systems Chemistry, 2010, 1, 1, 114
doi:10.1186/1759220814 bibtex 
A graphbased toy model of chemistry
Gil Benkö, Christoph Flamm, Peter F Stadler
In Journal of Chemical Information and Computer Sciences, 2003, 43, 4, 10851093
doi:10.1021/ci0200570 bibtex 
kinfold  Kinetic folding of RNA
The program Kinfold simulates the stochastic folding kinetics of RNA sequences into secondary structures. The algorithm operates on the basis of the formation, dissociation, and the shifting of individual base pairs. For the energy evaluation of RNA secondary structures Kinfold uses routines from the Vienna RNA Package and is also distributed with the package.
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Publications
probA  Stochastic pairwise sequence alignment
probA enables global pairwise alignment using the partition function over all canonical alignments to calculate the probability of every match between a position in the first and a position in the second sequence. For the calculation of the partition function we used a modified alignment algorithm that avoids the generation of solutions that are represented differently but are equivalent from a semantic point of view. Furthermore we include a parameter governing the relative weight of alignment paths with different scores (Kschischo 2000) and extend previous approaches to stochastic pairwise alignments by a stochastic backtracking procedure that can be used to obtain ensembles of suboptimal alignments with correct statistical weights.
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Publications
RNAwolf
The RNAwolf algorithm provides extended RNA secondary structure predictions. In extended secondary structures, each nucleotide can engage in a pairing with up two other nucleotides. Furthermore the paired edge (WatsonCrick, Sugar, Hoogsteen) for each nucleotide is predicted.
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Publications
A Folding Algorithm for Extended RNA Secondary Structures
Höner zu Siederdissen, Christian and Bernhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L.
Bioinformatics, 2011, 27, 129136
doi:10.1093/bioinformatics/btr220 bibtex 
RNApredator  Prediction of bacterial sRNA targets
The RNApredator software facilitates the prediction of sRNAmRNA interactions in bacteria. Currently targets can be searched in more than 1300 bacterial species. RNApredator uses a dynamic programming approach to compute putative targets. The main machinery used by RNApredator to find targets is the program called RNAplex. RNAplex is a new approach for RNARNA interaction search, which has a prediction accuracy similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup and IntaRNA. This is achieved by using a combination of precomputed accessibility profiles, with an approximate energy model, allowing to mimic the effects of the competition between intra and intermolecular interactions.
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RNApredator: fast accessibilitybased prediction of sRNA targets
Florian Eggenhofer, Hakim Tafer, Peter F Stadler, Ivo L Hofacker
In Nucleic Acids Research, 2011, 39, Web Server issue, W149W154
doi:10.1093/nar/gkr467 bibtex 
RNAstrand  Plus/Minus strand prediction of structured RNAs
The RNAstrand web server predicts the reading direction (plus or minus strand) of a structured RNA in a multiple sequence alignment.
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Publications
RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments
Kristin Reiche and Peter F. Stadler,
In Algorithms for Molecular Biology, 2007, 2, 6
doi:10.1186/1748718826 bibtex 
RNAxs  siRNA design
RNAxs will help you to design potent siRNAs to knock down your gene(s) of interest. RNAxs is based on the RNAplfold program to assess the mRNA target site accessibility. RNAxs was trained on two different datasets, one targeting 3'UTRs and the other one designed to repress coding sequences only.
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Publications
The impact of target site accessibility on the design of effective siRNAs.
Hakim Tafer, Stefan L Ameres, Gregor Obernosterer, Christoph A Gebeshuber, Renée Schroeder, Javier Martinez, Ivo L Hofacker
In Nature Biotechnology, 2008, 26, 5, 578583
10.1038/nbt1404 bibtex 
RNAz  Noncoding RNA prediction
RNAz detects functional RNA secondary structures in multiple sequence alignment based on two characteristic features: (i) thermodynamic stability, (ii) structural conservation.
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Publications
Fast and reliable prediction of noncoding RNAs
Stefan Washietl, Ivo L. Hofacker, and Peter F. Stadler
In Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 24542459
doi:10.1073/pnas.0409169102 bibtex 
Secondary structure prediction for aligned RNA sequences
Hofacker IL, Fekete M, and Stadler PF
In Journal of Molecular Biology, 2002, 319, 10591066
doi:10.1016/S00222836(02)00308X bibtex 
SOSlib  The SBML ODE Solver Library
SOSlib is both a programming library and a commandline application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivityenabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and nonstiff ODE systems.
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The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm
In Bioinformatics, 2006, 22, 11, 14061407
doi:10.1093/bioinformatics/btl086 bibtex 
Structure Conservation Analysis
The Structure Conservation Analysis web server will help you to detect evolutionarily conserved RNA secondary structures in multiple sequence alignments.
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treekin  Folding dynamics via numerical integration
The program treekin computes folding dynamics based on a given rate matrix. Usually, it operates on coarse grained versions of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macrostate. treekin reads in the a list of local minima (macrostates) and effective refolding rates between these minima as computed by barriers rates. Since the the number of macrostates is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix).
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Publications
Efficient computation of RNA folding dynamics
Michael T Wolfinger, W Andreas SvrcekSeiler, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
In Journal of Physics A: Mathematical and General, 2004, 37, 17, 47314741
doi:10.1088/03054470/37/17/005 bibtex 
Vienna Atlas of Viral RNA Structures
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Publications
Conserved RNA secondary structures in viral genomes: a survey.
Ivi L. Hofacker, Peter F. Stadler, and Roman R. Stocsits
In Bioinformatics, 2004, 20, 10, 14951499
doi:10.1093/bioinformatics/bth108 bibtex 
Vienna Reaction Network Library (ViennaRNL)
The Vienna Reaction Network Library ViennaRNL implements basic settheoretic operations on chemical reaction networks. It provides basic ANSI C data structures for chemical reactions and their networks, operations such as the union, intersection, or difference of chemical reaction networks.
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