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            "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": [
                "Web application",
                "Command-line tool"
            ],
            "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": [
                        "Primary contact"
                    ],
                    "name": "GenOuest",
                    "email": "support@genouest.org",
                    "url": "http://www.genouest.org",
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                    "gridid": null,
                    "typeEntity": "Person",
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                },
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                    "name": "GenOuest",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "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": 280,
            "name": "Paraload",
            "description": "Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed.",
            "homepage": "ftp://doua.prabi.fr/pub/logiciel/paraload",
            "biotoolsID": "Paraload",
            "biotoolsCURIE": "biotools:Paraload",
            "tool_type": [],
            "collection": [],
            "scientific_topics": [],
            "primary_publication": [],
            "operating_system": [],
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            "tool_licence": null,
            "documentation": null,
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            "last_update": "2019-11-06T12:00:30Z",
            "teams": [
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            ],
            "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_3407",
                "http://edamontology.org/topic_0154",
                "http://edamontology.org/topic_0602"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "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": 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_0621",
                "http://edamontology.org/topic_0654"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btab688"
            ],
            "operating_system": [],
            "tool_credit": [
                {
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                        "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,
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            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2021-11-01T10:14:54.337479Z",
            "teams": [
                "South Green"
            ],
            "source_repository": null
        },
        {
            "id": 289,
            "name": "PanAbyss",
            "description": "PanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.",
            "homepage": "https://github.com/Pange31/PanAbyss",
            "biotoolsID": "panabyss",
            "biotoolsCURIE": "biotools:panabyss",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_0160",
                "http://edamontology.org/topic_0080"
            ],
            "primary_publication": [],
            "operating_system": [
                "Windows",
                "Mac",
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Graziani",
                    "email": "fabien.graziani@inrae.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0009-0002-3966-0906",
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Graziani",
                    "email": "fabien.graziani@inrae.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0009-0002-3966-0906",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenoToul bioinformatics facility",
                    "email": null,
                    "url": "https://bioinfo.genotoul.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://github.com/Pange31/PanAbyss/wiki",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2026-08-25T11:50:05.748155Z",
            "teams": [
                "Genotoul-bioinfo"
            ],
            "source_repository": "https://github.com/Pange31/PanAbyss"
        },
        {
            "id": 292,
            "name": "Pan1c",
            "description": "Pan1c is a Snakemake workflow that simplifies the creation of pangenomes by focusing on the comparison of similar chromosomes, using either PGGB or Minigraph-Cactus.\nA pangenome graph is first generated individually for each chromosome, and then these chromosome-scale pangenomes are concatenated into a final graph. This approach reduces construction time through parallelization and facilitates interpretation as well as downstream analyses. Throughout the process, various graphs and statistics are produced to help users assess the quality of the pangenome graph and interpret the results.\nAll these visualizations and statistics are accessible via a web page generated by Pan1c-view.",
            "homepage": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c",
            "biotoolsID": "pan1c",
            "biotoolsCURIE": "biotools:pan1c",
            "tool_type": [
                "Workflow"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_3796"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Alexis Mergez",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Martin Racoupeau",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Philippe Bardou",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-0004-0251",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Christophe Klopp",
                    "email": "christophe.klopp@inrae.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-7126-5477",
                    "gridid": null,
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                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenoToul bioinformatics facility",
                    "email": null,
                    "url": "https://bioinfo.genotoul.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c/-/wikis/home",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2026-08-25T11:40:00.095755Z",
            "teams": [],
            "source_repository": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c"
        },
        {
            "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": [
                "Bioinformatics portal",
                "Web API",
                "Web application",
                "Workflow"
            ],
            "collection": [
                "Animal and Crop Genomics",
                "Galaxy"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0085",
                "http://edamontology.org/topic_3673",
                "http://edamontology.org/topic_0622",
                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_0196"
            ],
            "primary_publication": [
                "10.1093/nar/gkw343",
                "10.1093/nar/gkac247"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Galaxy Community",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Consortium",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Galaxy support",
                    "email": null,
                    "url": "https://biostar.usegalaxy.org/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "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": [
                "South Green"
            ],
            "source_repository": "https://github.com/galaxyproject/galaxy"
        },
        {
            "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
        }
    ]
}