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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 "phyclust" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'phyclust: Phylogenetic Clustering (Phyloclustering)'
version: 0.1-34
identifiers:
- type: doi
  value: 10.32614/CRAN.package.phyclust
abstract: Phylogenetic clustering (phyloclustering) is an evolutionary Continuous
  Time Markov Chain model-based approach to identify population structure from molecular
  data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides
  a convenient implementation of phyloclustering for DNA and SNP data, capable of
  clustering individuals into subpopulations and identifying molecular sequences representative
  of those subpopulations. It is designed in C for performance, interfaced with R
  for visualization, and incorporates other popular open source programs including
  ms (Hudson 2002) <https://doi.org/10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut
  and Grassly 1997) <https://doi.org/10.1093/bioinformatics/13.3.235>, Hap-Clustering
  (Tzeng 2005) <https://doi.org/10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007)
  <https://doi.org/10.1093/bioinformatics/13.5.555>, <https://doi.org/10.1093/molbev/msm088>,
  for simulating data, additional analyses, and searching the best tree. See the phyclust
  website for more information, documentations and examples.
authors:
- family-names: Chen
  given-names: Wei-Chen
  email: wccsnow@gmail.com
- family-names: Dorman
  given-names: Karin
preferred-citation:
  type: manual
  title: Overlapping Codon Model, Phylogenetic Clustering, and Alternative Partial
    Expectation Conditional Maximization Algorithm
  authors:
  - family-names: Chen
    given-names: Wei-Chen
    email: wccsnow@gmail.com
  journal: Ph.D. Diss., Iowa Stat University
  year: '2011'
repository: https://snoweye.r-universe.dev
repository-code: https://github.com/snoweye/phyclust
commit: 3f82c7bc4f328ba3b07f50cd82eb09997f00fc17
url: https://snoweye.github.io/phyclust/
date-released: '2023-09-03'
contact:
- family-names: Chen
  given-names: Wei-Chen
  email: wccsnow@gmail.com