---
# How to cite macsyfinder
# below the citation informations in yaml format

authors:
    - Néron Bertrand
    - Denise Rémi
    - Coluzzi Charles
    - Touchon Marie
    - Rocha Eduardo PC.
    - Abby Sophie
    -
date: 2023
title: "MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes."
journal:
    title: Peer Community Journal
    volume: 3
    enumber: e28
doi: 10.24072/pcjournal.250
url: https://peercommunityjournal.org/articles/10.24072/pcjournal.250/


# below a more human readable and traditional version

# Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S.
# MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes.
# Peer Community Journal, Volume 3 (2023), article no. e28.
# doi : 10.24072/pcjournal.250.
# https://peercommunityjournal.org/articles/10.24072/pcjournal.250/

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Biology",
  "author": [
    {
      "id": "https://orcid.org/0000-0002-0220-0482",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France "
      },
      "email": "bneron@pasteur.fr",
      "familyName": "Néron",
      "givenName": "Bertrand"
    },
    {
      "id": "https://orcid.org/0000-0002-5231-3346",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": " Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France "
      },
      "email": "sophie.abby@univ-grenoble-alpes.fr",
      "familyName": "Abby",
      "givenName": "Sophie"
    },
    {
      "id": "https://orcid.org/0000-0001-7704-822X",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "erocha@pasteur.fr",
      "familyName": "Rocha",
      "givenName": "Eduardo"
    }
  ],
  "codeRepository": "https://github.com/gem-pasteur/macsyfinder",
  "contributor": [
    {
      "id": "https://orcid.org/0000-0002-7552-1009",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France "
      },
      "email": "hmenager@pasteur.fr",
      "familyName": "Ménager",
      "givenName": "Hervé"
    },
    {
      "id": "https://github.com/fjossandon",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Biome Makers Inc."
      },
      "email": "fco.j.ossandon@gmail.com",
      "familyName": "Ossandon",
      "givenName": "Franscisco J,"
    },
    {
      "id": "https://orcid.org/0000-0003-2277-689X",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "APC Microbiome Institute: Cork, IE "
      },
      "familyName": "Denise",
      "givenName": "Rémi"
    },
    {
      "id": "https://orcid.org/0000-0001-7389-447X",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "mtouchon@pasteur.fr",
      "familyName": "Touchon",
      "givenName": "Marie"
    },
    {
      "id": "https://orcid.org/0000-0003-4797-6185",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "aperrin@pasteur.fr",
      "familyName": "Perrin",
      "givenName": "Amandine"
    },
    {
      "id": "https://orcid.org/0000-0002-0930-8920",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Université Paris Cité, SeqBio, Paris, France "
      },
      "email": "yoann.dufresne@pasteur.fr",
      "familyName": "Dufresne",
      "givenName": "Yoann"
    },
    {
      "id": "https://github.com/TrellixVulnTeam",
      "type": "Person",
      "email": "charles.mcfarland@trellix.com",
      "givenName": "TrellixVulnTeam"
    },
    {
      "id": "https://orcid.org/0000-0002-2961-9670",
      "type": "Person",
      "email": "crusoe@debian.org",
      "familyName": "Crusoe",
      "givenName": "Michael R."
    }
  ],
  "dateCreated": "2013-11-04",
  "dateModified": "2024-07-30",
  "datePublished": "2014-10-17",
  "description": "MacSyFinder is a program to model and detect macromolecular systems, genetic pathways… in prokaryotes protein datasets.",
  "downloadUrl": "https://pypi.org/project/MacSyFinder/",
  "funder": {
    "type": "Organization",
    "name": "Institut Pasteur Paris"
  },
  "keywords": [
    "bioinformatics",
    "functional genomics",
    "gene functional annotation"
  ],
  "license": "https://spdx.org/licenses/GPL-3.0+",
  "name": "macsyfinder",
  "operatingSystem": [
    "Linux",
    "BSD",
    "macOS"
  ],
  "programmingLanguage": "Python",
  "relatedLink": [
    "https://pypi.org/project/MacSyFinder/",
    "https://hub.docker.com/r/gempasteur/macsyfinder"
  ],
  "softwareRequirements": [
    "Python >= 3.10",
    "hmmer >= 3.1"
  ],
  "version": "2.1.4",
  "codemeta:contIntegration": {
    "id": "https://github.com/gem-pasteur/macsyfinder/actions"
  },
  "continuousIntegration": "https://github.com/gem-pasteur/macsyfinder/actions",
  "developmentStatus": "active",
  "issueTracker": "https://github.com/gem-pasteur/macsyfinder/issues",
  "referencePublication": "https://doi.org/10.24072/pcjournal.250"
}