# --------------------------------------------
# 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 "dowser" in publications use:'
type: software
license: AGPL-3.0-only
title: 'dowser: B Cell Receptor Phylogenetics Toolkit'
version: 2.2.1.999
doi: 10.1371/journal.pcbi.1009885
identifiers:
- type: doi
  value: 10.32614/CRAN.package.dowser
abstract: 'Provides a set of functions for inferring, visualizing, and analyzing B
  cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral
  sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize
  trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect
  biased ancestor-descendant relationships among metadata types Workflow examples
  available at documentation site (see URL). Citations: Hoehn et al (2022) <https://doi.org/10.1371/journal.pcbi.1009885>,
  Hoehn et al (2021) <https://doi.org/10.1101/2021.01.06.425648>.'
authors:
- family-names: Hoehn
  given-names: Kenneth
  email: kenneth.b.hoehn@dartmouth.edu
- family-names: Kleinstein
  given-names: Steven
  email: steven.kleinstein@yale.edu
preferred-citation:
  type: article
  title: Phylogenetic analysis of migration, differentiation, and class switching
    in B cells.
  authors:
  - family-names: Hoehn
    given-names: Kenneth B.
  - family-names: Pybus
    given-names: Oliver G.
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2022'
  journal: PLoS Computational Biology
  url: https://doi.org/10.1371/journal.pcbi.1009885
  doi: 10.1371/journal.pcbi.1009885
repository: https://kbhoehn.r-universe.dev
repository-code: https://bitbucket.org/kleinstein/dowser
commit: 8fee25495232abfc3d03aac8d5c46725c6b64a8c
url: https://dowser.readthedocs.io
date-released: '2024-05-21'
contact:
- family-names: Hoehn
  given-names: Kenneth
  email: kenneth.b.hoehn@dartmouth.edu
references:
- type: article
  title: Human B cell lineages associated with germinal centers following influenza
    vaccination are measurably evolving.
  authors:
  - family-names: Hoehn
    given-names: Kenneth B.
  - family-names: Turner
    given-names: Jackson S.
  - family-names: Miller
    given-names: Frederick I.
  - family-names: Jiang
    given-names: Ruoyi
  - family-names: Ellebedy
    given-names: Ali H.
  - family-names: Pybus
    given-names: Oliver G.
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2021'
  journal: eLife
  url: https://elifesciences.org/articles/70873
  doi: 10.7554/eLife.70873
- type: article
  title: Repertoire-wide phylogenetic models of B cell molecular evolution reveal
    evolutionary signatures of aging and vaccination.
  authors:
  - family-names: Hoehn
    given-names: Kenneth B.
  - family-names: Heiden
    given-names: Jason A.
    name-particle: Van der
  - family-names: Zhou
    given-names: Julian Q.
  - family-names: Lunter
    given-names: Gerton
  - family-names: Pybus
    given-names: Oliver G.
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2019'
  journal: PNAS
  url: https://doi.org/10.1073/pnas.1906020116
  doi: 10.1073/pnas.1906020116