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# 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 "aphylo" in publications use:'
type: software
license: MIT
title: 'aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic
  Trees'
version: 0.3-4
doi: 10.1371/journal.pcbi.1007948
identifiers:
- type: doi
  value: 10.32614/CRAN.package.aphylo
abstract: Implements a parsimonious evolutionary model to analyze and predict gene-functional
  annotations in phylogenetic trees as described in Vega Yon et al. (2021) <https://doi.org/10.1371/journal.pcbi.1007948>.
  Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled
  phylogenetic models, including thousands (hundreds) of annotations (trees) in the
  same run. The package also provides the tools for visualization of annotated phylogenies,
  calculation of posterior probabilities (prediction) and goodness-of-fit assessment
  featured in Vega Yon et al. (2021).
authors:
- family-names: Vega Yon
  given-names: George
  email: g.vegayon@gmail.com
  orcid: https://orcid.org/0000-0002-3171-0844
preferred-citation:
  type: article
  title: Bayesian parameter estimation for automatic annotation of gene functions
    using observational data and phylogenetic trees
  authors:
  - family-names: Vega Yon
    given-names: George
    email: g.vegayon@gmail.com
    orcid: https://orcid.org/0000-0002-3171-0844
  - family-names: Thomas
    given-names: Duncan
  - family-names: Morrison
    given-names: John
  - family-names: Mi
    given-names: Huaiyu
  - family-names: Thomas
    given-names: Paul
  - family-names: Marjoram
    given-names: Paul
  journal: PLOS Computational Biology
  year: '2021'
  month: '2'
  volume: '17'
  issue: '2'
  doi: 10.1371/journal.pcbi.1007948
  url: https://doi.org/10.1371/journal.pcbi.1007948
  issn: 1367-4803
  start: 1-35
repository: https://phylotastic.r-universe.dev
repository-code: https://github.com/USCbiostats/aphylo
commit: d11fc14f81e487ab0c0d41b47f97b6df582e1d57
url: https://github.com/USCbiostats/aphylo
contact:
- family-names: Vega Yon
  given-names: George
  email: g.vegayon@gmail.com
  orcid: https://orcid.org/0000-0002-3171-0844
references:
- type: manual
  title: Statistical Inference of Annotated Phylogenetic Trees
  authors:
  - family-names: Vega Yon
    given-names: George
    orcid: https://orcid.org/0000-0002-3171-0844
  notes: R package version 0.3-4
  url: https://github.com/USCBiostats/aphylo