Services

OpenMS is an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. 

OpenMS tool for the study of Protein-Protein interactions.

Open source software environment for development of biomedical data mining applications and data analysis workflows.

A service‐oriented environment for data mining, integrating web services as workflow components

A Galaxy instance customized for data-intensive computational analyses in microbiology and metagenomics.

OTP = "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final storage, execution of data quality monitoring programs, alignment of reads to the reference genome and variant calling. It allows full automatization, extended project administration, and full processing control for operators.

Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences;

A collection of software solutions for pangenome analyses.

To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs.

Software to identify defined fragments in biomacromolecules.

Our algorithm for identifying PCA-correlated SNPs takes as input a properly encoded SNP data matrix and outputs a score for each SNP. SNPs corresponding to the highest scores are typically the most informative in reproducing the structure of the population.

Bioinformatics Docker Images Project, a library of over 50 Docker images. 

PEP-FOLD4 is a service designed for the accurate and fast structure prediction of peptides containing fewer than 40 amino acids in aqueous solutions, particularly adapted to poly-charged peptides.

A platform for interpretation of proteomics identification results from multiple search engines.

Predictor of human deleterious Single Nucleotide Polymorphisms.

A binary classifier for predicting pathogenic variants in coding and non-coding regions.

phylogeny.fr is a web server intended to phylogenetic analyses.It has been designed to let non-specialist as well as expert users execute phylogenetic workflows. These workflows automatically chain programs to  perform different tasks: the identification of homologous sequences, their multiple alignment, the alignment curation, the phylogenetic reconstruction and the graphical representation of the inferred tree.

PHYLOViZ is a platform independent JAVA software that allows the analysis of sequence-based typing methods that generate allelic profiles and their associated epidemiological data.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.

A suite of tools available on the web to predict and analyze protein structure, function and mutations. 

A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source information and enables primary PPI dataset cross-checking. The PICKLE web-based interface allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein or the gene level, at three PPI filtering modes.

Pipeline for Cancer Inference

A pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes.

PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. 

An environment for NGS data management and analytics

Web-interface and database providing tools for the management of different plant phenotyping platforms, and the analysis of images and data.

Annotation of plant reference genomes and pangenomes, support and consulting.

Platon detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. It analyses the distribution bias of protein-coding gene families among chromosomes and plasmids.

An open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables.

A method for estimating the localization of transmembrane proteins in polarized cells

PoseView automatically creates two-dimensional diagrams of complexes with known 3D structure according to chemical drawing conventions.