Software produced by our group
Vienna RNA Package - Folding and comparing RNA secondary structures.
Ivo Hofacker, Christoph Flamm, Peter Schuster, Peter F. Stadler and many others.
A map of structural RNAs in the Human genome - ...
Stefan Washietl, Ivo L. Hofacker and Peter F. Stadler.
aln3nn - Progressive multiple sequence alignment with exact three-way dynamic programming steps.
Matthias Kruspe, Peter F. Stadler.
barriers - Basin Structure of Landscapes.
Christoph Flamm, Ivo Hofacker, Peter Stadler.
bbq - Discovering cis-regulatory modules.
Axel Mosig.
CartProduct - Creates Cartesian product graphs and decomposes given graphs into their prime factors w.r.t. the Cartesian product.
Marc Hellmuth, Marek Staude
codaln/code2aln - Progressive Multiple Alignments of Partially Coding Sequences.
Roman Stocsits, Ivo.L. Hofacker, Claudia Fried, Peter F. Stadler.
creto - A program for the determination of Cis-Regulatory Element Turn-Over rates.
Wolfgang Otto, Peter F. Stadler, Günter P. Wagner
cycdeco - Calculates a minimum cycle bases, the set of relevant cycles, the set of shortest and unique shortest and essential cycles, the interchangeability classes of relevant cycles for undirected unweighted graphs.
Petra Gleiss, Peter F. Stadler
cyclope - cyclope is a command-line tool for multiple circular sequence alignments.
Axel Mosig, Peter F. Stadler
fragrep - Efficient Search for Fragmented Patterns in Genomic Sequences.
Axel Mosig, Katrin Sameith, Peter F. Stadler.
FRANz - Reconstruction of Pedigrees
Markus Riester, Peter F. Stadler, Konstantin Klemm
GotohScan - Gene finding via semi-global alignment
Jana Hertel, Peter F. Stadler
HelixPSO - A Particle Swarm Optimizer (PSO) for RNA secondary structure prediction.
Michael Geis, Martin Middendorf
Kinwalker - An algorithm for prediction of RNA folding trajectories.
Michael Geis, Christoph Flamm, Michael Wolfinger, Andrea Tanzer, Ivo Hofacker, Christian Mandl, Peter F. Stadler, Martin Middendorf, Caroline Thurner
motifSearch - Detection of tertiary motifs in RNA secondary structure and sequence
Jana Hertel, Peter F Stadler and Ivo L Hofacker
NcDNAlign - Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller.
NetwPartLearn - A simulation tool for reverse engineering of genetic networks in case not all gene expression levels are known before transition.
Kristin Missal, Michael A. Cross, Dirk Drasdo
noisy - identify homo-plastic characters in multiple sequence alignments
Christoph Flamm, Sonja J Prohaska, Guido Fritzsch, Peter F Stadler
Proteinortho - Orthology detection tool
Marcus Lechner, Lydia Steiner, Sonja J. Prohaska
pwmatch - Recognizing Position Weight Matrix hits in a sequence.
Axel Mosig
quartm - Quartett Mapping Tool
Peter F. Stadler.
RNAmicro - Recoginizing microRNA Precursors in Comparative Genomics.
Jana Hertel, Peter F. Stadler.
RNAstrand - Predicts reading direction of structured RNAs in multiple sequence alignments.
KristinReiche, Peter F. Stadler
segemehl - fast short read mapping with indels
Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia Sharma, Jörg Vogel, Philipp Khaitovitch, Peter F. Stadler, Jörg Hackermüller
SnoReport - Computational identification of snoRNAs with unknown targets.
Jana Hertel, Ivo L. Hofacker and Peter F. Stadler.
SoupViewer - Graphical analysis tool for the output of the RNAsoup program
Jan Engelhardt, Kristin Reiche, Peter F. Stadler
StrongProduct - Decomposes given graphs into its prime factors w.r.t. the strong product.
Marc Hellmuth
SynBlast - Assisting the analysis of conserved synteny information
Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska
ToyChem - A Computational Toolkit Implementing a Realistic Articial Chemistry Model. [Web-Service]
Gil Benkö, Christoph Flamm
Useful software by other groups
- Software produced at TBI in Vienna (or by TBI people)







