Tools services

Name Description ELIXIR Node

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

ELIXIR Czech Republic

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

ELIXIR Denmark

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. 

ELIXIR Norway

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. 

ELIXIR Switzerland

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

ELIXIR Czech Republic

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.

ELIXIR Estonia

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.  

ELIXIR Netherlands

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. 

ELIXIR Finland

System for identification of alterations using protein mass spectrometry.

ELIXIR Czech Republic

Web interface for assignment and analysis of DNA conformers.

ELIXIR Czech Republic

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

ELIXIR Switzerland

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

ELIXIR Estonia

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

ELIXIR France

GraphWeb is a public web server for graph-based analysis of biological networks.

ELIXIR Estonia

HAMAP is a system for the classification and functional annotation of protein sequences. It consists of a collection of expert curated family profiles for protein classification and associated rules for protein annotation. 

ELIXIR Switzerland

Web server for identification of hot spots in protein engineering.

ELIXIR Czech Republic

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

ELIXIR France

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

ELIXIR Czech Republic

International Reference Center for Prokaryotic Insertion Sequences (IS) is a public database and a research tool that provides a list of insertion sequences (IS) isolated from bacteria and archae.

ELIXIR France

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets.

ELIXIR Switzerland

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

ELIXIR Estonia

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

ELIXIR Estonia

The META-pipe pipeline for annotation and analysis of marine metagenomics samples provides insight into phylogenetic diversity and metabolic and functional potential of environmental communities.

ELIXIR Norway

Interactive viewer of metadynamics results.

ELIXIR Czech Republic

MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. 

ELIXIR France

Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies.

ELIXIR Czech Republic

Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis.

ELIXIR Czech Republic

Web based application to validate ligand structure in PDB.

ELIXIR Czech Republic

A tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution.  It uses nearest neighbour DNA binding thermodynamics to estimate unwanted pairings between PCR samples.

ELIXIR Estonia

Software to identify defined fragents in biomacromolecules.

ELIXIR Czech Republic

PhyML (Phylogenetic inference using Maximum Likelihood) implements a heuristic algorithm to build phylogenetic trees from the analysis of genetic sequences in a sound statistical framework.

ELIXIR France

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.

ELIXIR Czech Republic

Primer3 is a program for designing PCR primers and oligos. 

ELIXIR Estonia

Set of tools and a web server for complex characterization of repetitive DNA based on data from next generation of sequence reads.

ELIXIR Czech Republic

Web tool for prediction of rRNA secondary structures.

ELIXIR Czech Republic

Web server for RNA structure comparison.

ELIXIR Czech Republic

Web application to compare multiple protein structural motifs.

ELIXIR Czech Republic

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

ELIXIR Estonia

SWISS-MODEL is a fully automated service for protein structure homology modelling. It provides a personal web based workspace for interactive modelling, storing project data and visualizing results online. 

ELIXIR Switzerland

A web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets (tracks), making use of statistical hypothesis testing and other advanced methodology.

ELIXIR Norway