HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 233,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=-maturity",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=-maturity",
"results": [
{
"id": 246,
"name": "LSD",
"description": "Fast dating using least-squares criteria and algorithms",
"homepage": "http://www.atgc-montpellier.fr/LSD/",
"biotoolsID": "lsdate",
"biotoolsCURIE": "biotools:lsdate",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:10:18.382414Z",
"teams": [],
"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_3173",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0749"
],
"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": [],
"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
},
{
"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
}
],
"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/"
},
{
"id": 58,
"name": "Crispi",
"description": "A CRISPR Interactive database.",
"homepage": "http://crispi.genouest.org/",
"biotoolsID": "crispi",
"biotoolsCURIE": "biotools:crispi",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0160"
],
"primary_publication": [
"10.1093/bioinformatics/btp586"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "GenOuest platform",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": null,
"documentation": "http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:06:25.068541Z",
"teams": [],
"source_repository": null
},
{
"id": 275,
"name": "IMGT 3Dstructure-DB",
"description": "IMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).\nAnnotation is based on the IMGT-ONTOLOGY concepts.",
"homepage": "http://www.imgt.org/3Dstructure-DB/",
"biotoolsID": "imgt_3dstructure",
"biotoolsCURIE": "biotools:imgt_3dstructure",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3930",
"http://edamontology.org/topic_3948",
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0804"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie-Paule Lefranc",
"email": "marie-paule.lefranc@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Patrice Duroux",
"email": "patrice.duroux@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Sofia Kossida",
"email": "sofia.kossida@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:15.256998Z",
"teams": [
"IMGT"
],
"source_repository": null
},
{
"id": 117,
"name": "AuReMe",
"description": "A unified workspace built around a Python package PADMet (Python library for hAndling metaData of METabolism), to house the reconstruction of genome-scale metabolic models.",
"homepage": "http://aureme.genouest.org",
"biotoolsID": "aureme",
"biotoolsCURIE": "biotools:aureme",
"tool_type": [
"Command-line tool",
"Workbench",
"Workflow"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1371/journal.pcbi.1006146"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "anne.siegel@inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://aureme.genouest.org/aureme.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:31.744031Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 36,
"name": "Banana Genome Hub",
"description": "A Next-Generation Information System for Musa genomics",
"homepage": "https://banana-genome-hub.southgreen.fr/",
"biotoolsID": "Banana_Genome_Hub",
"biotoolsCURIE": "biotools:Banana_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Gaëtan Droc",
"email": "gaetan.droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Mathieu Rouard",
"email": "m.rouard@cgiar.org",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Bioversity International",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "ANR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "CIRAD",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://banana-genome-hub.southgreen.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:38.690746Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 150,
"name": "BioMAJ",
"description": "BioMAJ is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.",
"homepage": "http://biomaj.genouest.org/",
"biotoolsID": "biomaj",
"biotoolsCURIE": "biotools:biomaj",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/bioinformatics/btn325"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "GenOuest platform",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Sallou",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "http://biomaj.readthedocs.io/en/latest/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T16:17:07.096336Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 120,
"name": "Cocoa Genome Hub",
"description": "The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.",
"homepage": "https://cocoa-genome-hub.southgreen.fr/",
"biotoolsID": "Cocoa_Genome_Hub",
"biotoolsCURIE": "biotools:Cocoa_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.1186/s12864-017-4120-9"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Argout",
"email": "xavier.argout@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-0100-5511",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Droc",
"email": "gaetan.droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lanaud",
"email": "claire.lanaud@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-6411-7310",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "CIRAD",
"email": null,
"url": "https://www.cirad.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "ANR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://api.tripal.info/api/tripal/3.x",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:43.154205Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 4,
"name": "Coffee Genome Hub",
"description": "The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.",
"homepage": "https://coffee-genome-hub.southgreen.fr/",
"biotoolsID": "Coffee_Genome_Hub",
"biotoolsCURIE": "biotools:Coffee_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gku1108"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Alexis Dereeper",
"email": "alexis.dereeper@ird.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Gaetan Droc",
"email": "droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://coffee-genome.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:58:58.975865Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 166,
"name": "CRAC",
"description": "CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.",
"homepage": "http://crac.gforge.inria.fr",
"biotoolsID": "crac",
"biotoolsCURIE": "biotools:crac",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0114",
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3320"
],
"primary_publication": [
"10.1186/gb-2013-14-3-r30"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "For question regarding the software",
"email": "crac-bugs@lists.gforge.inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "For questions, comments, remarks on the algorithm or the article",
"email": "crac-article@lists.gforge.inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "CECILL-2.0",
"documentation": "http://crac.gforge.inria.fr/documentation/",
"maturity": "Mature",
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:59Z",
"teams": [
"ATGC",
"Bilille"
],
"source_repository": null
},
{
"id": 277,
"name": "IMGT mAb-DB",
"description": "IMGT/mAb-DB is the IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA).\nIMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.",
"homepage": "http://www.imgt.org/mAb-DB/",
"biotoolsID": "IMGT_mAb-DB",
"biotoolsCURIE": "biotools:IMGT_mAb-DB",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3400",
"http://edamontology.org/topic_3930",
"http://edamontology.org/topic_3948",
"http://edamontology.org/topic_0804"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "Marie-Paule Lefranc",
"email": "marie-paule.Lefranc@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Sofia Kossida",
"email": "sofia.Kossida@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Patrice Duroux",
"email": "patrice.duroux@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/mAb-DB/doc",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T13:59:20.810745Z",
"teams": [
"IMGT"
],
"source_repository": null
},
{
"id": 57,
"name": "AnnotQTL",
"description": "Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.",
"homepage": "http://annotqtl.genouest.org/",
"biotoolsID": "annotqtl",
"biotoolsCURIE": "biotools:annotqtl",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0085"
],
"primary_publication": [
"10.1093/nar/gkr361"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "GenOuest",
"email": "support@genouest.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": null,
"documentation": "http://annotqtl.genouest.org/tutorial",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:06:26.428724Z",
"teams": [],
"source_repository": null
},
{
"id": 85,
"name": "ARIA",
"description": "A software for automated NOE assignment and NMR structure calculation.",
"homepage": "http://aria.pasteur.fr/",
"biotoolsID": "aria",
"biotoolsCURIE": "biotools:aria",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"Institut Pasteur",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_1317",
"http://edamontology.org/topic_0176",
"http://edamontology.org/topic_3306",
"http://edamontology.org/topic_3332",
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0081",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_0593"
],
"primary_publication": [
"10.1093/bioinformatics/btl589"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "http://aria.pasteur.fr/contact-info",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Michael Nilges",
"email": "michael.nilges@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Benjamin Bardiaux",
"email": "benjamin.bardiaux@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "http://aria.pasteur.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:37:34.670261Z",
"teams": [],
"source_repository": null
},
{
"id": 135,
"name": "Askomics",
"description": "AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL",
"homepage": "https://github.com/askomics",
"biotoolsID": "askomics",
"biotoolsCURIE": "biotools:askomics",
"tool_type": [
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3366"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Olivier Dameron",
"email": "olivier.dameron@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Filangi",
"email": "olivier.filangi@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Anthony Bretaudeau",
"email": "anthony.bretaudeau@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "https://github.com/askomics/askomics",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2025-06-09T11:52:30.706337Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 168,
"name": "FastME",
"description": "Distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ. It includes Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.",
"homepage": "http://www.atgc-montpellier.fr/fastme/",
"biotoolsID": "fastme",
"biotoolsCURIE": "biotools:fastme",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"galaxyPasteur",
"FastME"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/molbev/msv150"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 300,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T20:59:19.988087Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 158,
"name": "Fpocket",
"description": "Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket",
"biotoolsID": "fpocket",
"biotoolsCURIE": "biotools:fpocket",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0166"
],
"primary_publication": [
"10.1186/1471-2105-10-168"
],
"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/fpocket/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 2470,
"last_update": "2024-11-24T20:59:53.208420Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 146,
"name": "fqtools",
"description": "A package that provides tools for efficient FASTQ files manipulation.",
"homepage": "https://bioweb.pasteur.fr/packages/pack@fqtools@1.1",
"biotoolsID": "fqtools",
"biotoolsCURIE": "biotools:fqtools",
"tool_type": [
"Suite"
],
"collection": [
"fqtools"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Maintainer"
],
"name": "Nicolas Joly",
"email": "njoly@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-06-16T10:55:24Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README"
},
{
"id": 160,
"name": "Frog",
"description": "Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.",
"homepage": "https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2",
"biotoolsID": "frog2",
"biotoolsCURIE": "biotools:frog2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkq325"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Frederic Guyon",
"email": "frederic.guyon@univ-paris-diderot.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Maria A. Miteva",
"email": "maria.mitev@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"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/Frog2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 6400,
"last_update": "2026-03-19T13:27:15.551602Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 101,
"name": "Genomicus-plants",
"description": "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "https://www.genomicus.biologie.ens.fr/genomicus-plants",
"biotoolsID": "Genomicus-Plants",
"biotoolsCURIE": "biotools:Genomicus-Plants",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1156",
"10.1093/pcp/pcu177"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"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
}
]
}