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.

blockbuster - Detect blocks of overlapping reads using a gaussian-distribution approach

David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovitch, Peter F Stadler

CartProduct - Creates Cartesian product graphs and decomposes given graphs into their prime factors w.r.t. the Cartesian product.

Marc Hellmuth, Marek Staude

clasp - A fast local fragment chainer using sum-of-pair gap costs

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler.

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

galculator - Nucleotide frequency counter

Marcus Lechner, Peter F. Stadler

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

LocalStrongPFD - (Approximate) Prime Factor Decomposition of Strong Product Graphs Using a Local Approach

Marc Hellmuth

MiTFi - Mitochondrial tRNA finder

Frank Jühling, Joern Pütz, Matthias Bernt, Alexander Donath, Martin Middendorf, Catherine Florentz, Peter F. Stadler

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

PLEXY - Target prediction for Box C/D snoRNAs

Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler and Hakim Tafer

POFF - Orthology detection tool combining clustering and synteny

Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thevenin, Jens Stoye, Sonja J. Prohaska, Peter F. Stadler

POFF - Orthology detection tool combining clustering and synteny

Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thevenin, Jens Stoye, Sonja J. Prohaska, 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.

RNAplex - RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.

Hakim Tafer

RNAsnoop - RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence.

Hakim Tafer

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

StoChDyn - Stochastic modeling of chromatin state dynamics across cell divisions

Christian Arnold, Peter F. Stadler, Sonja J. Prohaska

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

TARGETING - An efficient solver for the Maximal Pairing Problem on arbitrary trees

Christian Arnold, Peter F. Stadler

TileShuffle - Statistical analysis of tiling array expression data

Christian Otto, Kristin Reiche, Jörg Hackermüller

ToyChem - A Computational Toolkit Implementing a Realistic Articial Chemistry Model. [Web-Service]

Gil Benkö, Christoph Flamm

Tracker 2 - A tool for footprint detection and alignment consistency determination

Wolfgang Otto, Peter F. Stadler and Sonja J Prohaska


Useful software by other groups