# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "PhyloProfile" in publications use:'
type: software
license: MIT
title: 'PhyloProfile: PhyloProfile'
version: 2.4.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.PhyloProfile
abstract: PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic
  profiles, presence/absence patterns of genes over a set of species, are commonly
  used to trace the functional and evolutionary history of genes across species and
  time. With PhyloProfile we can enrich regular phylogenetic profiles with further
  data like sequence/structure similarity, to make phylogenetic profiling more meaningful.
  Besides the interactive visualisation powered by R-Shiny, the package offers a set
  of further analysis features to gain insights like the gene age estimation or core
  gene identification.
authors:
- family-names: Tran
  given-names: Vinh
  email: tran@bio.uni-frankfurt.de
  orcid: https://orcid.org/0000-0001-6772-7595
- family-names: Greshake Tzovaras
  given-names: Bastian
  email: bgreshake@googlemail.com
- family-names: Ebersberger
  given-names: Ingo
  email: ebersberger@bio.uni-frankfurt.de
preferred-citation:
  type: unpublished
  title: PhyloProfile v2 - Exploring multi-layered phylogenetic profiles at scale
  authors:
  - name: Vinh Tran
  - name: Ingo Ebersberger
  year: '2025'
  notes: 'Preprint available at arXiv: https://doi.org/10.48550/arXiv.2504.19710'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/BIONF/PhyloProfile
commit: 92deab474c3613e4311396168c4921b857837446
url: https://github.com/BIONF/PhyloProfile/
date-released: '2026-06-01'
contact:
- family-names: Tran
  given-names: Vinh
  email: tran@bio.uni-frankfurt.de
  orcid: https://orcid.org/0000-0001-6772-7595
references:
- type: article
  title: 'PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic
    profiles'
  authors:
  - name: Ngoc-Vinh Tran
  - name: Bastian Greshake Tzovaras
  - name: Ingo Ebersberger
  journal: Bioinformatics
  year: '2018'
  volume: 34(17)
  url: https://doi.org/10.1093/bioinformatics/bty225
  start: 3041-3043
  doi: 10.1093/bioinformatics/bty225