produced by our group
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. StadlerA map of structural RNAs in the Human genome
Stefan Washietl, Ivo L. Hofacker and Peter F. Stadleraln3nn
— Progressive multiple sequence alignment with exact three-way dynamic programming steps Matthias Kruspe, Peter F. Stadlerbarriers
— Basin Structure of Landscapes Christoph Flamm, Ivo Hofacker, Peter StadlerBAT
— A modular bisulfite analysis toolkit (BAT). It tackles the major tasks for analyzing bisulfite sequencing data Helene Kretzmer, Christian Otto, Steve Hoffmannbbq
— Discovering cis-regulatory modules Axel Mosigblockbuster
— Detect blocks of overlapping reads using a gaussian-distribution approach David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovitch, Peter F StadlerCartProduct
— Creates Cartesian product graphs and decomposes given graphs into their prime factors w.r.t. the Cartesian product Marc Hellmuth, Marek Staudeclasp
— A fast local fragment chainer using sum-of-pair gap costs Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadlercodaln/code2aln
— Progressive Multiple Alignments of Partially Coding Sequences Roman Stocsits, Ivo.L. Hofacker, Claudia Fried, Peter F. Stadlercreto
— A program for the determination of Cis-Regulatory Element Turn-Over rates Wolfgang Otto, Peter F. Stadler, Günter P. Wagnercycdeco
— 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. Stadlercyclope
— cyclope is a command-line tool for multiple circular sequence alignments Axel Mosig, Peter F. StadlerDIEGO
— differential alternative splicing detection in RNASeq data Gero Doose, Stephan H Bernhart, Rabea Wagener und Steve HoffmannePoPE
— Efficient Prediction of Paralog Evolution Jana Hertel and Peter F. Stadlerfragrep
— Efficient Search for Fragmented Patterns in Genomic Sequences. Axel Mosig, Katrin Sameith, Peter F. StadlerFRANz
— Reconstruction of Pedigrees Markus Riester, Peter F. Stadler, Konstantin Klemmgalculator
— Nucleotide frequency counter Marcus Lechner, Peter F. StadlerGeneralized ADP
— A collection of Haskell libraries making life easy for dynamic programmers Christian Hoener zu Siederdissen et al.GotohScan
— Gene finding via semi-global alignment Jana Hertel, Peter F. StadlerHelixPSO
— A Particle Swarm Optimizer (PSO) for RNA secondary structure prediction Michael Geis, Martin MiddendorfKinwalker
— 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 ThurnerLazyB Assembly with MuCHSALSA
— Fast and cheap genome assembly Thomas Gatter, Sarah von Löhneysen, Kevin KleinLocalStrongPFD
— Approximate) Prime Factor Decomposition of Strong Product Graphs Using a Local Approach Marc Hellmuthmetilene
— Fast and sensitive detection of differential DNA methylation Frank Jühling, Helene Kretzmer, Stephan H. Bernhart, Christian Otto, Peter F. Stadler & Steve Hoffmann
Link to the Software
Here you can find a de.NBI customer satisfaction survey