Software

haarz

— A Simple Data-Adaptive Probabilistic Variant Calling Model
Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer

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Sierra Platinum

— The first webserver for multi-replicate peak-calling
Lydia Müller, Daniel Gerighausen, Mariam Farman and Dirk Zeckzer

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Vienna RNA Package

— Folding and comparing RNA secondary structures
Ivo Hofacker, Christoph Flamm, Peter Schuster, Peter F. Stadler and many others.

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Asymmetry

— A Flexible Python Package for the Simulation of Complex Gene Family Histories
David Schaller, Marc Hellmuth, Peter F. Stadler

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A map of structural RNAs in the Human genome

Stefan Washietl, Ivo L. Hofacker and Peter F. Stadler

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aln3nn

— Progressive multiple sequence alignment with exact three-way dynamic programming steps
Matthias Kruspe, Peter F. Stadler

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barriers

— Basin Structure of Landscapes
Christoph Flamm, Ivo Hofacker, Peter Stadler

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BAT

— A modular bisulfite analysis toolkit (BAT). It tackles the major tasks for analyzing bisulfite sequencing data
Helene Kretzmer, Christian Otto, Steve Hoffmann

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bbq

— Discovering cis-regulatory modules
Axel Mosig

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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

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CartProduct

— Creates Cartesian product graphs and decomposes given graphs into their prime factors w.r.t. the Cartesian product
Marc Hellmuth, Marek Staude

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clasp

— A fast local fragment chainer using sum-of-pair gap costs
Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler

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codaln/code2aln

— Progressive Multiple Alignments of Partially Coding Sequences
Roman Stocsits, Ivo.L. Hofacker, Claudia Fried, Peter F. Stadler

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creto

— A program for the determination of Cis-Regulatory Element Turn-Over rates
Wolfgang Otto, Peter F. Stadler, Günter P. Wagner

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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

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cyclope

— cyclope is a command-line tool for multiple circular sequence alignments
Axel Mosig, Peter F. Stadler

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DIEGO

— differential alternative splicing detection in RNASeq data
Gero Doose, Stephan H Bernhart, Rabea Wagener und Steve Hoffmann

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ePoPE

— Efficient Prediction of Paralog Evolution
Jana Hertel and Peter F. Stadler

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fragrep

— Efficient Search for Fragmented Patterns in Genomic Sequences.
Axel Mosig, Katrin Sameith, Peter F. Stadler

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FRANz

— Reconstruction of Pedigrees
Markus Riester, Peter F. Stadler, Konstantin Klemm

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galculator

— Nucleotide frequency counter
Marcus Lechner, Peter F. Stadler

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Generalized ADP

— A collection of Haskell libraries making life easy for dynamic programmers
Christian Hoener zu Siederdissen et al.

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GotohScan

— Gene finding via semi-global alignment
Jana Hertel, Peter F. Stadler

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HelixPSO

— A Particle Swarm Optimizer (PSO) for RNA secondary structure prediction
Michael Geis, Martin Middendorf

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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

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LazyB Assembly with MuCHSALSA

— Fast and cheap genome assembly
Thomas Gatter, Sarah von Löhneysen, Kevin Klein

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LocalStrongPFD

— Approximate) Prime Factor Decomposition of Strong Product Graphs Using a Local Approach
Marc Hellmuth

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metilene

— Fast and sensitive detection of differential DNA methylation
Frank Jühling, Helene Kretzmer, Stephan H. Bernhart, Christian Otto, Peter F. Stadler & Steve Hoffmann

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MiTFi

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

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motifSearch

— Detection of tertiary motifs in RNA secondary structure and sequence
Jana Hertel, Peter F Stadler and Ivo L Hofacker

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NcDNAlign

— Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller.

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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

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noisy

— Identify homo-plastic characters in multiple sequence alignments
Christoph Flamm, Sonja J Prohaska, Guido Fritzsch, Peter F Stadler

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PLEXY

— Target prediction for Box C/D snoRNAs
Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler and Hakim Tafer

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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

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Proteinortho

— Orthology detection tool
Marcus Lechner, Lydia Steiner, Sonja J. Prohaska

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pwmatch

— Recognizing Position Weight Matrix hits in a sequence

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quartm

— Quartett Mapping Tool
Peter F. Stadler

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RNAmicro

— Recoginizing microRNA Precursors in Comparative Genomics
Jana Hertel, Peter F. Stadler

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RNAplex

— RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs
Hakim Tafer

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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

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RNAstrand

— Predicts reading direction of structured RNAs in multiple sequence alignments
Kristin Reiche, Peter F. Stadler

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Ryuto

— Network-Flow based Transcriptome Reconstruction
Thomas Gatter, Peter F. Stadler

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segemehl

— Fast short read mapping with indels
Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia Sharma, Jörg Vogel, Philipp Khaitovitch, Peter F. Stadler, Jörg Hackermüller

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SMORE

— Synteny Modulator of Repetitive Elements
Sarah J. Berkemer, Anne Hoffmann, Cameron R. A. Murray and Peter F. Stadler

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SnoReport

— Computational identification of snoRNAs with unknown targets
Jana Hertel, Ivo L. Hofacker and Peter F. Stadler

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SoupViewer

— Graphical analysis tool for the output of the RNAsoup program
Jan Engelhardt, Kristin Reiche, Peter F. Stadler

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StoChDyn

— Stochastic modeling of chromatin state dynamics across cell divisions
Christian Arnold, Peter F. Stadler, Sonja J. Prohaska

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StrongProduct

— Decomposes given graphs into its prime factors w.r.t. the strong product
Marc Hellmuth

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Svhip

— Flexible classifier retraining for de novo detection of non-coding RNAs
Christopher Klapproth

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SynBlast

— Assisting the analysis of conserved synteny information
Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska

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TARGETING

— An efficient solver for the Maximal Pairing Problem on arbitrary trees
Christian Arnold, Peter F. Stadler

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TileShuffle

— Statistical analysis of tiling array expression data
Christian Otto, Kristin Reiche, Jörg Hackermüller

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ToyChem

— A Computational Toolkit Implementing a Realistic Articial Chemistry Model
Gil Benkö, Christoph Flamm

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Tracker 2

— A tool for footprint detection and alignment consistency determination
Wolfgang Otto, Peter F. Stadler and Sonja J Prohaska

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Software produced at TBI in Vienna

TBI

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