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Welcome to the DOWNLOAD page of the 'Applied Bioinformatics' group.

Download ARB, the most sophisticated software environment for molecular sequence data management, comprehensive molecular sequence analysis, phylogenetic treeing, and probe/primer design. ARB is developed in a team of computer scientists and microbiologists at the TUM, and regularly updated.
Source code and binaries of the latest stable release
Source code and binaries - latest build
ARB rRNA databases
Latest rRNA databases - ARB Silva project

Download RAxML, the ultimative software for high performance calculation of phylogenetic trees from nucleic acid alignments based on Maximum Likelihood. RAxML is developed within the projekt KONWIHR PARBAUM. It is an implementation of the currently fastest algorithm for maximum likelihood based phylogenentic treeing. Download RAxML

ChipChecker is a software for the interpretations of signal reads from fluorecence images which have been recorded in DNA-Chip experiments. It will identify positive and negative bits (actually fluorescent spots) on the chip, interprete the pattern and translate it into a list of identified microorganisms or genes, analog to a BIT-interpreter. The binary and the source code of ChipChecker can be downloaded and run with provided test data. ChipChecker has been developed by Jens Ernst (Lehrstuhl für effiziente Algorithmen, TU München; ernstj@in.tum.de) and Harald Meier (Lehrstuhl für Rechnertechnik und Rechnerorganisation, TU München; meierh@in.tum.de). If questions or problems occur, please refer to us.

CHIPDESIGNER is a GUI-based implementation of an algorithm for designing oligonucleotide probe sets for DNA-Chips from nucleic acid databases. The algorithm and a basic implementation has been introduced at the IPDPS2003 (workshop HICOMB2003). The proceedings paper "Accurate Method for Fast Design of Diagnostic Oligonucleotide Probe Sets for DNA Microarrays" can be found by Citeseer when searching for the authors (--> PUBLICATIONS). For giving proof to the applicability of our program different oligonucleotide probe sets have been designed from a large 16S rRNA database for interesting groups of interesting environmental bacteria. These probe sets are proposals for DNA microarrays, and their quality would have to be evaluated in the laboratory experiment first. The authors are not responsible for any negative results that has been achieved by using these probes in a laboratory experiments, as experimental effects which cannot be predicted by a computer. Take a look at the calculated probe sets, here.