ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. 

Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts

Atomic Charge Calculator - web application using the Electronegativity Equalization Method.

AuReMe, is an adaptable workspace for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. It is adapted to the metabolic study of non-conventional organisms and microbiomes to ensure that the process is reproducible and documented regardless of the combination of tools used. Among others, modules included in the AuReMe environment are a model-management PADmet module, a wiki-export module, a gap-filling tool for non-conventional organism (meneco), a tool for the reduction of microbial communities based on metabolic complementarities (miscoto) and a package to handle the analysis of large-scale microbiota (Metage2Metabo).

Predicts the subcellular localization of proteins in eukaryotes.

Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis

Web portal for tools registry and discovery, incorporating tool benchmarking and service monitoring information and the use of EDAM for precise scientific tool description. 

Build, test and convert Cloud and HPC software into Linux containers.

The BioXSD / GTrack ecosystem is an infrastructure of generic state-of-the-art data formats for integrative bioinformatics, with focus on genomics and epigenomics, sequence and structure bioinformatics, and other applications. 

 BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection).  They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with  (ODC-By) v1.0 license.

BUSCO provides quantitative measures for the assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

A resource for analyzing and interpreting genetic dependencies in cancer.

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

Multiple Sequence Alignment package via on-line server, in collaboration with groups in Germany, the UK and France.

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

A server for calculating contact maps of X-ray, NMR and predicted structures.

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.  

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

System for identification of alterations using protein mass spectrometry.

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

Web interface for assignment and analysis of DNA conformers.

Tool to predict backbone dynamics from a single protein sequence

R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images. In the context of high-throughput microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. Part of the Human Omics Analysis Toolbox