Software

picture:CSI:FingerIDCSI:FingerID searches a tandem mass spectrum of a small compound (metabolite) in a molecular structure database such as PubChem. It combines fragmentation trees (combinatorics and maximum a posteriori estimation) with molecular fingerprints (machine learning), making it possibly the strongest search engine that is currently out there. It will search different databases for molecular structures.

picture:SIRIUSWe present Sirius, a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database. More…

passatutto enables the assessment of confidence in a match for metabolomics mass spectral library search. The tool allows both, to use either an empirical Bayes or a target-decoy approach. Different methods to construct the decoy database can be used, all of them avoiding to construct “decoy metabolite structures”. In addition, passatutto can be used for noise-filtering reference spectra based on fragmentation trees. More…

picture:Gecko3Gecko3 searches genomes for the co-appearances of genes, called gene clusters. Different from other tools, Gecko3 is capable of handling 500+ bacterial genomes, allows for imperfect occurrences and occurrences in arbitrary subsets of the genomes, does not assume the order of genes in the gene cluster to be conserved, does not force gene clusters to be monophyletic, comes with a sound statistical analysis (p-values) for each gene cluster, and ships with a graphical user interface. More…

The Greedy Strict Consensus Merger (GSCM) Project is a java library and command line tool providing the greedy strict consensus merger supertree algorithm for rooted input trees. It provides several scoring functions to determine in which oder the input trees get merged. Combining different scorings is also implemented as well as a randomized version of the algorithm. For more detailed information about the algorithm see the Literature.

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COCONUT is a tool for estimating the composition distribution from mass spectra of synthetic copolymers. It is based on Linear Programming and is capable of automatically resolving overlapping isotopes and isobaric ions. It also features spectral pre-processing methods: baseline correction, spectral smoothing and peak picking (centroiding). COCONUT provides an easy-to-use graphical user interface. More…

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PLUMS is a software that analyses tandem mass spectra of synthetic polymers. It helps to identify monomer repeating units and fragmentation series of homopolymers. The end groups of the fragment ions are determined without any further knowledge of the polymer class or the fragmentation mechanism. More…

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MoLE is a tool for estimating heavy isotope incorporations of molecules based on mass spectrometry data. The program comes with an easy-to-use graphical user interface, and allows for batch processing of mass spectra. More…

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We present EPoS, a modular software framework for phylogenetic analysis and visualization. Existing phylogenetic software can be split into two groups. Algorithmic packages that provide computational methods for a specific problem, and visualization tools to analyse results. Many algorithmic tools lack in us ability, as they are often command line based, while visualizations often suffer from poor graphical user interfaces. EPoS fills this gap by combining a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations and data structures. A consistent interface is used to manage data or to start available computational methods, disconnecting the work flow from the data or applied methods.More…

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PEACE (Parameterized and Exact Algorithms for Cluster Editing) is a project for clustering experimental data using a weighted graph derived from pairwise similarity information.
The underlying mathematical model is the NP-complete Cluster Editing problem. Similar models are used in the clustering algorithms CLICK and CAST. Advantages are that you do not have to specify cluster centers, the number of clusters need not be given in advance, and solutions are definite. We compute exact solutions for this model, mainly with fixed-parameter algorithms. These algorithms employ both parameter-independent and parameter-dependent reduction rules to cut down the size of the instance initially and inside the search tree. PEACE is implemented in C++. More…

Molecule graph of phenylalanineBond order information is essential for many applications in chemistry.  Unfortunately, this information is omitted in many data formats of molecule graphs. We present a java-based program that computes bond order assignments of molecule graphs using a penalty function as suggested by Wang et al. (2006). This program implements our tree decomposition-based dynamic programming algorithm introduced in Böcker et al. 2009. A C++ implementation of our algorithm will be integrated in the Biochemical Algorithms Library (BALL). More…

Decomp is a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises in mass spectrometry when we know the molecular mass of a protein, DNA, or metabolite fragment but have no other information. Decomp employs efficient algorithms for computing such decompositions. Decomp is supplied with an easy-to-use web interface that allows users to modify all important parameters. Results can be used either independently or as a starting point for further evaluations in the identification pipeline of unknown sample fragments. (Joint work with Zs. Lipták, M. Martin, H. Sudek)