Tools

Tools

52 tools, softwares, databases and websites available      
  • AlienTrimmer – Alexis Criscuolo A tool for trimming and clipping FASTQ file
  • Aria web – Fabien Mareuil Hervé Ménager, Benjamin Bardiaux Web interface for determination of structure by NMR
  • Bacnet – Christophe Bécavin BACNET is a Java based platform to develop website for multi-omics analysis.
  • Bioservices – Thomas Cokelear Python package that provides access to many Bioinformatics Web Services.
  • BMGE – Alexis Criscuolo A tool for selecting characters or encoding character states from a multiple sequence alignment for phylogenetic inference
  • Booster – Frédéric Lemoine An alternative method for calculating the branch supports of phylogenetic trees, using the bootstrap
  • BPM – Yoann Dufresne Tool for rapid bacterial strain identification
  • C2A / A2C – Alexis Criscuolo Two tools for translating and back-translating codon and amino-acid sequence files, respectively
  • CapsuleDB – Bertrand Néron Website to query over 2,000 capsule systems on 2,786 chromosomes and 2,087 plasmids of 2,484 bacterial and 159 archaeal fully sequenced genomes
  • checkmyindex – Hugo Varet A tool for testing illumina index compatibility for barcoding
  • coGSEA – Natalia Pietrosemoli, Maxime Borry Comparative Gene Set Enrichment Analysis. R package Gene Set Enrichment Analysis and comparison among methods coGSEA
  • Comat – Gael Millot A tool for 2 by 2 comparison of contingency matrices of same dimension in batches
  • Concatenate – Alexis Criscuolo A tool for building supermatrices of characters by concatenating multiple sequence alignments
  • CONJscan – Julien Guglielmini, Eduardo Rocha, jean Cury, Bertrand Néron, Olivia Doppelt-Azeroual Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles
  • contig_info – Alexis Criscuolo A tool for estimating descriptive statistics from de novo genome assembly
  • CP4P – Quentin Giai Gianetto Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values
  • CRAW – Bertrand Néron, Christophe Malabat A tool for extracting NGS coverage of specific region and visualize it
  • CRC mapper – Violaine Saint-Andrè Build Core Regulatory Circuitry from H3K27ac ChIP-seq data
  • CRISPRCasFinder – Bertrand Néron Tool and a database allowing the identification of both CRISPR arrays and Cas proteins.
  • CWL standard – Hervé Ménager Specification for describing analysis workflows and tools in a way that makes them portable and scalable
  • DreamTools -Thomas Cokelaer DREAMTools aims at sharing code used in the scoring of DREAMchallenges
  • EDAM ontology – Bryan Brancotte, Hervé Ménager The ontology of Bioinformatics operations, types of data, data identifiers, data formats, and topics
  • eFASTA – Alexis Criscuolo A tool for extracting a nucleotide segment from a FASTA-formatted file
  • ELIXIR Tools Platform – bio.tools – Kenzo-Hugo Hillion, Hervé Ménager Improve the discovery, quality and sustainability of software resources
  • FASTA2AGP – Alexis Criscuolo A tool to convert a FASTA-formatted scaffold file into an AGP one
  • findSynapomorphies – Julien Guglielmini A tool to find characters shared by a group of aligned sequences
  • Galaxy – Olivia Doppelt-Azeroual, Fabien Mareuil, Kenzo-Hugo Hillion, Hervé Ménager The Institut Pasteur Galaxy instance. Open to all user, from pasteur or not
  • gbk2ENA – Mélanie Hennart, Alexis Criscuolo A tool to convert Genbank files into EMBL-like files suitable for submission to the ENA
  • Gklust – Alexis Criscuolo Fast greedy clustering of genomes based on minhash similarity
  • goalign/gotree – Frédéric Lemoine GoTree is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language
  • GRAAL – Romain Koszul, Christophe Zimmer, Alex Cournac, Martial, Marbouty A software to reconstruct 1D genome structures from 3D contact data obtained from Hi-C experiments.
  • imp4p – Quentin Giai Gianetto R package for Imputation for Proteomics
  • Institut Pasteur MLST – Julien Guglielmini, Sylvain Brisse A website that hosts databases of (core-genome) MultiLocus Sequence Typing (MLST) schemes for bacterial strain genotyping
  • IntegronFinder – Bertrand Néron Bioinformatics tool to finds integrons in DNA sequences
  • iPPI-DB – Rachel Torchet, Hervé Ménager, Fabien Mareuil, Olivia Dopplet-Azeroual A web application for the maintenance and curation of Protein-protein interaction data
  • JASS – Pierre Lechat, Vincent Guillemot, Hervé Ménager, Hanna Julienne JASS is an online tool for the joint analysis of GWAS summary statistics
  • JolyTree – Alexis Criscuolo A tool for the fast inference of distance-based phylogenetic trees from unaligned genome sequences
  • Listeriomics – Christophe Bécavin, Nicolas Maillet, Pierre Lechat Interactive web platform to browse genomic, transcriptomic and proteomic datasets in Listeria
  • MacSyFinder / MacSyView – Bertrand Néron Tools for the detection of macromolecular systems in protein datasets using systems modelling and similarity search
  • MemHDX – Stevenn Volant A tool for proteomic analysis
  • merlin linkage analysis – Gael Millot An integrated bash & R script for SNP array/pedigree linkage analysis using the TARS cluster
  • Meta3C – Romain Koszul a metagenomic chromosome conformation capture
  • NGphylogeny – Frédéric Lemoine, Damien Correia, Olivier Gascuel A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences
  • PastML – Anna Zhukova, Sohta Ishikawa, Olivier Gascuel PastML is a tool for ancestral character reconstruction on phylogenetic trees
  • PCM – Amine Ghozlane A tool for the identification of resistance gene using 3D modeling
  • PF2heatmaps – Hugo Varet A tool for creating heatmaps after differential analysis
  • Phylogeny.fr – Fredéric Lemoine, Damien Correia, Olivier Gascuel Reference phylogenetic markers (along with multiple sequence alignments and position specific scoring matrices) that are well-suited for bacterial tree reconstruction
  • PhyloM: bacteria – Alexis Criscuolo Reference phylogenetic markers (along with multiple sequence alignments and position specific scoring matrices) that are well-suited for bacterial tree reconstruction
  • PhyloM: NCLDV – Julien Guglielmini Reference phylogenetic markers (along with multiple sequence alignments and position specific scoring matrices) that are well-suited for Nucleocytoplasmic large DNA virus (NCLDV) tree reconstruction
  • ProteoDiffMQ – Quentin Giai Gianetto Differential analysis of label-free proteomic experiments from MaxQuant
  • qaf_demux – Blaise Li A tool for demultiplexing FASTQ files with barcode included into the read and checking quality
  • ReGaTe – Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager Software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry
  • REQ – Alexis Criscuolo A tool for estimating a confidence value at each branch of a phylogenetic tree from a matrix of pairwise evolutionary distances
  • RPG – Nicolas Maillet Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-induced cleavage sites on amino acid sequences
  • RVDB-prot – Thomas Bigot Reference viral coding sequence and associated HMM database developed for enhancing virus detection from HTS data
  • Salmonella CRISPR Typing – Kenzo-Hugo Hillion Tool to subtype Salmonella strains
  • SARTools – Hugo Varet, Marie-Agnès Dillies A R package for differential analysis with normalisation by DESeq2 or edgeR
  • Sequana / Sequanix – Thomas Cokelear, Dimitri Desvilleschabrol, Rachel Legendre Set of Snakemake HTS pipelines and graphical interface
  • SHAMAN – Amine Ghozlane, Stevenn Volant, Pierre Lechat A tool for quantitative metagenomic analysis with a graphical interface
  • SHERPA – Natalia Pietrosemoli SHiny ExploRation tool for transcriPtomic Analysis. Interactive web platform for Transcriptomic dataset exploration
  • SynTView – Pierre Lechat Dynamic Browser for Microbial Synteny and Polymorphism Information