GET /api/tool/?format=api&offset=140&ordering=description
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 216,
    "next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=description",
    "previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=description",
    "results": [
        {
            "id": 113,
            "name": "ParameciumDB",
            "description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
            "homepage": "https://paramecium.i2bc.paris-saclay.fr",
            "biotoolsID": "parameciumdb",
            "biotoolsCURIE": "biotools:parameciumdb",
            "tool_type": [
                "Database portal"
            ],
            "collection": [
                "elixir-fr-sdp-2019"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0621",
                "http://edamontology.org/topic_0089",
                "http://edamontology.org/topic_0080",
                "http://edamontology.org/topic_0160",
                "http://edamontology.org/topic_3321"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Contact Form",
                    "email": null,
                    "url": "https://paramecium.i2bc.paris-saclay.fr/cgi/user/contact",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Terms of Use",
                    "email": null,
                    "url": "https://paramecium.i2bc.paris-saclay.fr/parawiki/Terms_of_Use",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                }
            ],
            "tool_licence": "CC-BY-4.0",
            "documentation": null,
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-25T14:00:30.463079Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 148,
            "name": "Vidjil",
            "description": "Open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time.",
            "homepage": "http://www.vidjil.org/",
            "biotoolsID": "vidjil",
            "biotoolsCURIE": "biotools:vidjil",
            "tool_type": [
                "Web application",
                "Web interface",
                " Command-line"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0080",
                "http://edamontology.org/topic_0804"
            ],
            "primary_publication": [
                "10.1371/journal.pone.0172249"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Support",
                    "email": "contact@vidjil.org",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://github.com/vidjil/vidjil",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2018-12-10T12:58:58Z",
            "teams": [
                "Bilille"
            ],
            "source_repository": null
        },
        {
            "id": 176,
            "name": "Galaxy",
            "description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
            "homepage": "https://galaxyproject.org/",
            "biotoolsID": "galaxy",
            "biotoolsCURIE": "biotools:galaxy",
            "tool_type": [
                "Workflow",
                "Bioinformatics portal",
                "Web application",
                "Web API"
            ],
            "collection": [
                "Galaxy",
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_0085",
                "http://edamontology.org/topic_3673",
                "http://edamontology.org/topic_0196",
                "http://edamontology.org/topic_0622"
            ],
            "primary_publication": [
                "10.1093/nar/gkw343",
                "10.1093/nar/gkac247"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Galaxy support",
                    "email": null,
                    "url": "https://biostar.usegalaxy.org/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Galaxy Community",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Consortium",
                    "note": null
                }
            ],
            "tool_licence": "AFL-3.0",
            "documentation": "https://usegalaxy.org/api/docs",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 400,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T14:46:57.861339Z",
            "teams": [
                "ABiMS",
                "South Green"
            ],
            "source_repository": "https://github.com/galaxyproject/galaxy"
        },
        {
            "id": 261,
            "name": "Panache",
            "description": "Panache (Pangenome analyzer with chromosomal exploration) is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show aresence/absence information of pangenomic blocks of sequence or genes in a browser-like display.",
            "homepage": "http://github.com/SouthGreenPlatform/panache",
            "biotoolsID": "panache",
            "biotoolsCURIE": "biotools:panache",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0654",
                "http://edamontology.org/topic_0621"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btab688"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Mathieu Rouard",
                    "email": "m.rouard@cgiar.org",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-0284-1885",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Éloi Durant",
                    "email": "eloi.durant@ird.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-2734-4327",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": null,
            "maturity": null,
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2021-11-01T10:14:54.337479Z",
            "teams": [
                "South Green"
            ],
            "source_repository": null
        },
        {
            "id": 126,
            "name": "PanGeneHome",
            "description": "PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly.",
            "homepage": "http://pangenehome.lmge.uca.fr/",
            "biotoolsID": "PanGeneHome",
            "biotoolsCURIE": "biotools:PanGeneHome",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0602",
                "http://edamontology.org/topic_3407",
                "http://edamontology.org/topic_0154"
            ],
            "primary_publication": [],
            "operating_system": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "tool_credit": [],
            "tool_licence": null,
            "documentation": null,
            "maturity": null,
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T14:48:31.897688Z",
            "teams": [
                "AuBi"
            ],
            "source_repository": null
        },
        {
            "id": 175,
            "name": "Logol",
            "description": "Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).",
            "homepage": "http://logol.genouest.org",
            "biotoolsID": "logol",
            "biotoolsCURIE": "biotools:logol",
            "tool_type": [
                "Command-line tool",
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0160"
            ],
            "primary_publication": [
                "10.1007/978-3-319-09192-1_4"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenOuest",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "GenOuest",
                    "email": "support@genouest.org",
                    "url": "http://www.genouest.org",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "CECILL-2.0",
            "documentation": "http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=LOGOL",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2018-12-10T12:58:34Z",
            "teams": [
                "GenOuest"
            ],
            "source_repository": null
        },
        {
            "id": 163,
            "name": "PEP-FOLD",
            "description": "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.",
            "homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3",
            "biotoolsID": "pep-fold",
            "biotoolsCURIE": "biotools:pep-fold",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_2275"
            ],
            "primary_publication": [
                "10.1093/nar/gkp323",
                "10.1093/nar/gks419",
                "10.1093/nar/gkw329"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Pierre Tufféry",
                    "email": "pierre.tuffery@univ-paris-diderot.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1033-9895",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Freeware",
            "documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 3900,
            "citations": null,
            "annual_visits": 30000,
            "last_update": "2024-11-24T20:59:57.942237Z",
            "teams": [
                "RPBS"
            ],
            "source_repository": null
        },
        {
            "id": 161,
            "name": "PEP-SiteFinder",
            "description": "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.",
            "homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder",
            "biotoolsID": "pep-sitefinder",
            "biotoolsCURIE": "biotools:pep-sitefinder",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3534",
                "http://edamontology.org/topic_2275"
            ],
            "primary_publication": [
                "10.1093/nar/gku404"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Pierre Tufféry",
                    "email": "pierre.tuffery@univ-paris-diderot.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1033-9895",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Freeware",
            "documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 347,
            "citations": null,
            "annual_visits": 1482,
            "last_update": "2024-11-24T20:59:55.640056Z",
            "teams": [
                "RPBS"
            ],
            "source_repository": null
        },
        {
            "id": 208,
            "name": "MindTheGap",
            "description": "Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.",
            "homepage": "https://gatb.inria.fr/software/mind-the-gap/",
            "biotoolsID": "mindthegap",
            "biotoolsCURIE": "biotools:mindthegap",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "GATB"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0199"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btu545"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenOuest",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Claire Lemaitre",
                    "email": "claire.lemaitre@inria.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://gatb.inria.fr/software/mind-the-gap/",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:58:48.627968Z",
            "teams": [
                "GenOuest"
            ],
            "source_repository": null
        },
        {
            "id": 82,
            "name": "PhyML",
            "description": "Phylogenetic estimation software using Maximum Likelihood",
            "homepage": "https://www.atgc-montpellier.fr/phyml/",
            "biotoolsID": "phyml",
            "biotoolsCURIE": "biotools:phyml",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "PhyML",
                "galaxyPasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_0091"
            ],
            "primary_publication": [
                "10.1093/sysbio/syq010"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Support",
                        "Maintainer",
                        "Primary contact",
                        "Developer"
                    ],
                    "name": "Stephane Guindon",
                    "email": "guindon@lirmm.fr",
                    "url": "http://stephaneguindon.github.io/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "LIRMM",
                    "email": null,
                    "url": "http://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Developer",
                        "Maintainer",
                        "Support"
                    ],
                    "name": "Stephane Guindon",
                    "email": "guindon@lirmm.fr",
                    "url": "https://stephaneguindon.github.io/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "LIRMM",
                    "email": null,
                    "url": "https://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": "GPL-2.0",
            "documentation": "https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:34:19.190685Z",
            "teams": [
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 240,
            "name": "SMS",
            "description": "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.",
            "homepage": "http://www.atgc-montpellier.fr/sms/",
            "biotoolsID": "PhyMLSMS",
            "biotoolsCURIE": "biotools:PhyMLSMS",
            "tool_type": [
                "Command-line tool",
                "Web application"
            ],
            "collection": [
                "PhyML"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_2269"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [],
            "tool_licence": null,
            "documentation": "http://www.atgc-montpellier.fr/download/papers/sms-HowItWorks.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:59:18.380055Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 19,
            "name": "PhylOPDb",
            "description": "Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes.",
            "homepage": "http://g2im.u-clermont1.fr/phylopdb/help.php",
            "biotoolsID": "phylopdb",
            "biotoolsCURIE": "biotools:phylopdb",
            "tool_type": [
                "Database portal",
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0632",
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_3518"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": "pierre.peyret@udamail.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://g2im.u-clermont1.fr/phylopdb/help.php",
            "maturity": null,
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2018-12-10T12:58:58Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 131,
            "name": "jvenn",
            "description": "Plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams.",
            "homepage": "http://bioinfo.genotoul.fr/jvenn/",
            "biotoolsID": "jvenn",
            "biotoolsCURIE": "biotools:jvenn",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0092",
                "http://edamontology.org/topic_2269"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": "support.genopole@toulouse.inra.fr",
                    "url": "http://bioinfo.genotoul.fr/jvenn/index.html",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://jvenn.toulouse.inra.fr/app/index.html",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-25T14:53:20.499445Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 121,
            "name": "LoRDEC",
            "description": "Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.",
            "homepage": "http://www.atgc-montpellier.fr/lordec/",
            "biotoolsID": "lordec",
            "biotoolsCURIE": "biotools:lordec",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "elixir-fr-sdp-2019"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0654",
                "http://edamontology.org/topic_3168",
                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_0091"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Leena Salmela",
                    "email": "leena.salmela@cs.Helsinki.FI",
                    "url": "https://www.cs.helsinki.fi/u/lmsalmel/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Eric Rivals",
                    "email": "rivals@lirmm.fr",
                    "url": "http://www.lirmm.fr/~rivals/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "LIRMM",
                    "email": null,
                    "url": "http://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://www.atgc-montpellier.fr/lordec/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-25T14:01:03.046535Z",
            "teams": [
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 145,
            "name": "MacSyFinder",
            "description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.",
            "homepage": "https://github.com/gem-pasteur/macsyfinder",
            "biotoolsID": "macsyfinder",
            "biotoolsCURIE": "biotools:macsyfinder",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "GEM Pasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0085"
            ],
            "primary_publication": [
                "10.1371/journal.pone.0110726",
                "10.24072/pcjournal.250"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Bioinformatics and Biostatistics HUB",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Microbial Evolutionary Genomics Unit",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": "CNRS - UMR 352"
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/bertrand-neron/",
                    "orcidid": "https://orcid.org/0000-0002-0220-0482",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": "https://orcid.org/0000-0001-7704-822X",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Sophie Abby",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-5231-3346",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "https://research.pasteur.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "C3BI",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/center/c3bi/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "https://macsyfinder.readthedocs.io/en/latest/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T13:49:36.708539Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/gem-pasteur/macsyfinder"
        },
        {
            "id": 143,
            "name": "leBIBI",
            "description": "Quick bioInformatic phylogeny of prokaryotes.",
            "homepage": "https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgi",
            "biotoolsID": "leBIBI",
            "biotoolsCURIE": "biotools:leBIBI",
            "tool_type": [],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0084"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [],
            "tool_licence": null,
            "documentation": null,
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 154145,
            "last_update": "2019-11-06T11:33:13Z",
            "teams": [
                "PRABI-Lyon-Grenoble"
            ],
            "source_repository": null
        },
        {
            "id": 243,
            "name": "RAPPAS",
            "description": "RAPPAS stands for Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences. It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment.",
            "homepage": "http://www.atgc-montpellier.fr/RAPPAS/",
            "biotoolsID": "RAPPAS",
            "biotoolsCURIE": "biotools:RAPPAS",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_0637",
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_3174"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btz068"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Benjamin Linard",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://github.com/blinard-BIOINFO/RAPPAS",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:59:27.880847Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 92,
            "name": "RARe",
            "description": "RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms.\nThe purpose of this web portal is to facilitate the discoverability of these data. \nRARe search is an implementation of DataDiscovery.",
            "homepage": "https://urgi.versailles.inrae.fr/rare/",
            "biotoolsID": "RARe",
            "biotoolsCURIE": "biotools:RARe",
            "tool_type": [
                "Database portal",
                "Web service",
                "Web API",
                "Web application"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "URGI"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0780",
                "http://edamontology.org/topic_0610",
                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_3810"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Support",
                        "Primary contact"
                    ],
                    "name": "Support service",
                    "email": "urgi-support@inrae.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                }
            ],
            "tool_licence": "BSD-3-Clause",
            "documentation": "https://urgi.versailles.inrae.fr/rare/about",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2025-07-29T13:42:40.608985Z",
            "teams": [
                "URGI"
            ],
            "source_repository": null
        },
        {
            "id": 119,
            "name": "RSAT suite",
            "description": "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.",
            "homepage": "http://rsat.eu",
            "biotoolsID": "rsat",
            "biotoolsCURIE": "biotools:rsat",
            "tool_type": [
                "Web application",
                "Suite"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0621",
                "http://edamontology.org/topic_0749",
                "http://edamontology.org/topic_0203",
                "http://edamontology.org/topic_3512",
                "http://edamontology.org/topic_3125"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Jacques van Helden",
                    "email": "Jacques.van-Helden@univ-amu.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Other",
            "documentation": "http://rsat.eu",
            "maturity": null,
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-25T14:00:33.330732Z",
            "teams": [
                "TAGC-BU"
            ],
            "source_repository": null
        },
        {
            "id": 267,
            "name": "ReMap",
            "description": "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.",
            "homepage": "https://remap.univ-amu.fr/",
            "biotoolsID": "inserm-remap",
            "biotoolsCURIE": "biotools:inserm-remap",
            "tool_type": [
                "Database portal"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0102",
                "http://edamontology.org/topic_0160",
                "http://edamontology.org/topic_0749",
                "http://edamontology.org/topic_0204",
                "http://edamontology.org/topic_0085",
                "http://edamontology.org/topic_3173"
            ],
            "primary_publication": [
                "10.1093/nar/gku1280",
                "10.1093/nar/gkab996",
                "10.1093/nar/gkz945",
                "10.1093/nar/gkx1092"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Support"
                    ],
                    "name": "Inserm U1090 - TAGC",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Maintainer",
                        "Primary contact"
                    ],
                    "name": "Benoit Ballester",
                    "email": "benoit.ballester@inserm.fr",
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0002-0834-7135",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Aix-Marseille University",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "French Institute of Health and Medical Research",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://remap.univ-amu.fr/about_hsap_page",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:21:26.315951Z",
            "teams": [
                "TAGC-BU"
            ],
            "source_repository": "https://remap.univ-amu.fr/"
        }
    ]
}