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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 "scoup" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'scoup: Simulate Codons with Darwinian Selection Modelled as an OU Process'
version: 1.6.0
doi: 10.18129/B9.bioc.scoup
identifiers:
- type: doi
  value: 10.32614/CRAN.package.scoup
abstract: An elaborate molecular evolutionary framework that facilitates straightforward
  simulation of codon genetic sequences subjected to different degrees and/or patterns
  of Darwinian selection. The model is built upon the fitness landscape paradigm of
  Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno.
  This enables realistic evolutionary process of living organisms to be reproducible
  seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated
  herein. Consequently, otherwise complex biological processes, such as the effect
  of the interplay between genetic drift and fitness landscape fluctuations on the
  inference of diversifying selection, may now be investigated with minimal effort.
  Frequency-dependent and stochastic fitness landscape update techniques are available.
authors:
- family-names: Sadiq
  given-names: Hassan
  email: hassan.t.sadiq@gmail.com
  orcid: https://orcid.org/0000-0003-0192-7134
preferred-citation:
  type: manual
  title: 'scoup: Simulate Codon Sequences with Darwinian Selection Incorporated as
    an Ornstein-Uhlenbeck Process'
  authors:
  - family-names: Sadiq
    given-names: Hassan
    email: hassan.t.sadiq@gmail.com
    orcid: https://orcid.org/0000-0003-0192-7134
  notes: Bioconductor/R Package
  year: '2024'
  doi: 10.18129/B9.bioc.scoup
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/thsadiq/scoup
commit: d96f7cdc3bd1a28635114fe8d45aad19be6bf60a
url: https://github.com/thsadiq/scoup
date-released: '2026-03-17'
contact:
- family-names: Sadiq
  given-names: Hassan
  email: hassan.t.sadiq@gmail.com
  orcid: https://orcid.org/0000-0003-0192-7134
references:
- type: article
  title: 'scoup: Simulate Codon Sequences with Darwinian Selection Incorporated as
    an Ornstein-Uhlenbeck Process'
  authors:
  - family-names: Sadiq
    given-names: Hassan
  - family-names: Martin
    given-names: Darren P
  journal: Journal of Open Source Software
  year: '2026'
  volume: '11'
  issue: '119'
  doi: 10.21105/joss.09797
  start: '9797'