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