Services: Software Tools

Workflows and tools for analysis of microscopy image data and cellular phenotyping using Galaxy. Provision of expertise and support of projects requiring automatic image analysis.

Galaxy server dedicated towards public health applications: tools, pipelines and databases for using WGS in routine pathogen typing and characterization

An optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses. All code is open-source and freely available in the GEAR software repositories, including the code for the web server front-end applications and the backend genomics analysis software. Among other command-line applications, the backend code includes Tracy.

Prokaryote genome annotation system, modular, flexible and extensible.

Eukaryotic genome annotation system, modular, flexible and extensible.

GenExVis (Gene Expression Visualizer) is a desktop application for exploring and visualizing differential gene expression data. 

GenomeCRISPR is a database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).

The GenomeRNAi database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

GeoMine enables textual, numerical and 3D searching with full chemical awareness in binding sites of the entire PDB dataset. 

A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its qualitative dynamical behaviour.

Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins using profile Hidden Markov Models (pHMMs).

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

gtrellis is an R package which facilitates genome-level trellis layout, for enhancing visualisation and graphical layout

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. 

Performs haplotype assembly from long gapless reads.

Enables you to set up and train models for ab initio prediction of gene structure. That is, to perform "gene calling" and identify which base pairs in a genome belong to the UTR/CDS/Intron of genes.

HilbertCurve is an R package which generates 2D Hilbert curves for genomic and other data

A web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways. 

Estimation of transmembrane regions based on amino acid sequence

Web server for identification of hot spots in protein engineering.

A collection of web resources for working with proteins, drug reactions, gene expression analysis, proteome profiling and assessing MinION Data, including: 

• DeSeq2 - an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays
• DexSeq - an extension of DESeq for the analysis of alternative exon usage.
• EBImage - R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images.
• SMART - a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches.
• SIDER - a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions.

HyPPI classifies a protein-protein complex concerning its interaction type into a permanent, transient or crystal artifact. 

Predicts protein stability changes upon single point mutation from protein structure or protein sequence.

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to commonly used alternatives for false discovery rate (FDR) control by assigning data-driven weights to each hypothesis. The IHW software package provide a mechanism that allows the methodology to be applied to many different data types.

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. 

Web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server offers a variety of methods to explore nucleic acid flexibility, from coarse-grained low resolution mesoscopic models to atomistic molecular dynamics simulations.