phagefactor/CITATION.cff at master · TMs-code/phagefactor · GitHub

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cff-version: 1.2.0
title: "phageFACTor: structure-aware functional annotation of prophage genomes"
message: "If you use this software, please cite it and its dependencies."
type: software
authors:
  - given-names: Tanaïs, Jade
    family-names: Moreau
    affiliation: Institut Pasteur
license: MIT
repository-code: "https://github.com/TMs-code/phageFACTor"
keywords:
  - prophage
  - phage annotation
  - structural homology
  - FoldSeek
  - ProstT5
  - Phold

# ---------------------------------------------------------------------------
# Dependencies — please cite these too.
# ---------------------------------------------------------------------------
references:
  - type: article
    title: "Phold: the protein structure-based phage annotation tool"
    authors:
      - family-names: Bouras
        given-names: George
    doi: 10.1093/nar/gkaf1448
    notes: "Nucleic Acids Research, 2026 (verify on publication)."
  - type: article
    title: "Pharokka: a fast scalable bacteriophage annotation tool"
    authors:
      - family-names: Bouras
        given-names: George
    doi: 10.1093/bioinformatics/btac776
    repository-code: "https://github.com/gbouras13/pharokka"
  - type: article
    title: "Fast and accurate protein structure search with Foldseek"
    authors:
      - family-names: van Kempen
        given-names: Michel
      - family-names: Steinegger
        given-names: Martin
    doi: 10.1038/s41587-023-01773-0
    repository-code: "https://github.com/steineggerlab/foldseek"
  - type: article
    title: "Bilingual language model for protein sequence and structure (ProstT5)"
    authors:
      - family-names: Heinzinger
        given-names: Michael
      - family-names: Rost
        given-names: Burkhard
    doi: 10.1093/nargab/lqae150
    repository-code: "https://github.com/mheinzinger/ProstT5"
    notes: "NAR Genomics and Bioinformatics, 6(4):lqae150, 2024."
  - type: article
    title: "Synteny-aware functional annotation of bacteriophage genomes with Phynteny"
    authors:
      - family-names: Grigson
        given-names: Susanna R.
      - family-names: Edwards
        given-names: Robert A.
    doi: 10.1101/2025.07.28.667340
    repository-code: "https://github.com/susiegriggo/Phynteny_transformer"
    notes: "bioRxiv preprint, 2025."
  - type: article
    title: "eggNOG 6.0: enabling comparative genomics across 12 535 organisms (for pre-CDS-computed / host-annotated inputs)"
    authors:
      - family-names: Hernández-Plaza
        given-names: Ana
    doi: 10.1093/nar/gkac1022
    repository-code: "https://github.com/eggnogdb/eggnog-mapper"
    notes: "Nucleic Acids Research, 51(D1):D389–D394, 2023."