
@Manual{R-adegenet,
  title = {adegenet: Exploratory Analysis of Genetic and
    Genomic Data},
  author = {<NAME> and <NAME>},
  year = {2020},
  note = {R package version 2.1.3},
  url = {https://github.com/thibautjombart/adegenet},
}

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {<NAME> and <NAME> and <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME> and Damien {de Vienne}},
  year = {2020},
  note = {R package version 5.4-1},
  url = {http://ape-package.ird.fr/},
}

@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2020},
  url = {https://www.R-project.org/},
}

@Manual{R-BiocManager,
  title = {BiocManager: Access the Bioconductor Project
    Package Repository},
  author = {<NAME>},
  year = {2021},
  note = {R package version 1.30.12},
  url = {https://CRAN.R-project.org/package=BiocManager},
}

@Manual{R-Biostrings,
  title = {Biostrings: Efficient manipulation of biological
    strings},
  author = {<NAME> and <NAME> and <NAME> and <NAME>},
  year = {2020},
  note = {R package version 2.58.0},
  url = {https://bioconductor.org/packages/Biostrings},
}

@Manual{R-colorspace,
  title = {colorspace: A Toolbox for Manipulating and
    Assessing Colors and Palettes},
  author = {<NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME>},
  year = {2020},
  note = {R package version 2.0-0},
  url = {https://CRAN.R-project.org/package=colorspace},
}

@Manual{R-ips,
  title = {ips: Interfaces to Phylogenetic Software in R},
  author = {<NAME> and <NAME> and Franz-
    <NAME>},
  year = {2019},
  note = {R package version 0.0.11},
  url = {https://CRAN.R-project.org/package=ips},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with kable
    and Pipe Syntax},
  author = {<NAME>},
  year = {2021},
  note = {R package version 1.3.4},
  url = {https://CRAN.R-project.org/package=kableExtra},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic
    Report Generation in R},
  author = {<NAME>},
  year = {2021},
  note = {R package version 1.32},
  url = {https://yihui.org/knitr/},
}

@Manual{R-muscle,
  title = {muscle: Multiple Sequence Alignment with MUSCLE},
  author = {Algorithm by <NAME>. R port by <NAME>.
    Kalinka.},
  year = {2020},
  note = {R package version 3.32.0},
  url = {http://www.drive5.com/muscle/},
}

@Manual{R-phangorn,
  title = {phangorn: Phylogenetic Reconstruction and
    Analysis},
  author = {<NAME> and <NAME> and Leonardo
    {<NAME>} and <NAME> and <NAME>},
  year = {2021},
  note = {R package version 2.6.3},
  url = {https://github.com/KlausVigo/phangorn},
}

@Manual{R-r2symbols,
  title = {r2symbols: Symbols for Markdown and Shiny
    Application},
  author = {<NAME>},
  year = {2020},
  note = {R package version 0.1},
  url = {https://github.com/oobianom/r2symbols},
}

@Manual{R-readxl,
  title = {readxl: Read Excel Files},
  author = {<NAME> and <NAME>},
  year = {2019},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=readxl},
}

@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {<NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME> and
    <NAME>},
  year = {2021},
  note = {R package version 2.7},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-seqinr,
  title = {seqinr: Biological Sequences Retrieval and
    Analysis},
  author = {<NAME> and <NAME>},
  year = {2020},
  note = {R package version 4.2-5},
  url = {http://seqinr.r-forge.r-project.org/},
}

@Manual{R-seqRFLP,
  title = {seqRFLP: Simulation and visualization of
    restriction enzyme cutting pattern from DNA sequences.},
  author = {<NAME> and <NAME>},
  year = {2012},
  note = {R package version 1.0.1},
  url = {https://CRAN.R-project.org/package=seqRFLP},
}

@Manual{R-ShortRead,
  title = {ShortRead: FASTQ input and manipulation},
  author = {<NAME> and <NAME> and <NAME>},
  year = {2020},
  note = {R package version 1.48.0},
}

@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common
    String Operations},
  author = {<NAME>},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}

@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the
    Tidyverse},
  author = {<NAME>},
  year = {2021},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=tidyverse},
}

@Manual{R-XML,
  title = {XML: Tools for Parsing and Generating XML Within
    R and S-Plus},
  author = {Duncan {<NAME>}},
  year = {2021},
  note = {R package version 3.99-0.6},
  url = {http://www.omegahat.net/RSXML},
}

@Manual{R-XVector,
  title = {XVector: Foundation of external vector
    representation and manipulation in Bioconductor},
  author = {<NAME> and <NAME>},
  year = {2020},
  note = {R package version 0.30.0},
  url = {https://bioconductor.org/packages/XVector},
}

@Article{adegenet2008,
  title = {adegenet: a R package for the multivariate
    analysis of genetic markers},
  journal = {Bioinformatics},
  year = {2008},
  author = {<NAME>},
  volume = {24},
  pages = {1403-1405},
  doi = {10.1093/bioinformatics/btn129},
}

@Article{adegenet2011,
  title = {adegenet 1.3-1: new tools for the analysis of
    genome-wide SNP data},
  journal = {Bioinformatics},
  year = {2011},
  author = {<NAME> and <NAME>},
  doi = {10.1093/bioinformatics/btr521},
}

@Article{ape2019,
  title = {ape 5.0: an environment for modern phylogenetics
    and evolutionary analyses in {R}},
  author = {<NAME> and <NAME>},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
}

@Article{colorspace2020a,
  title = {{colorspace}: A Toolbox for Manipulating and
    Assessing Colors and Palettes},
  author = {<NAME> and <NAME> and <NAME> and <NAME> and <NAME> and <NAME> and <NAME> and <NAME>},
  journal = {Journal of Statistical Software},
  year = {2020},
  volume = {96},
  number = {1},
  pages = {1--49},
  doi = {10.18637/jss.v096.i01},
}

@Article{colorspace2009a,
  title = {Escaping {RGB}land: Selecting Colors for
    Statistical Graphics},
  author = {<NAME> and <NAME> and <NAME>},
  journal = {Computational Statistics \& Data Analysis},
  year = {2009},
  volume = {53},
  number = {9},
  pages = {3259--3270},
  doi = {10.1016/j.csda.2008.11.033},
}

@Article{colorspace2009b,
  title = {Somewhere over the Rainbow: How to Make Effective
    Use of Colors in Meteorological Visualizations},
  author = {<NAME> and <NAME> and <NAME> and <NAME>},
  journal = {Bulletin of the American Meteorological
    Society},
  year = {2009},
  volume = {96},
  number = {2},
  pages = {203--216},
  doi = {10.1175/BAMS-D-13-00155.1},
}

@Misc{ips2008 onwards,
  title = {PHYLOCH: R language tree plotting tools and
    interfaces to diverse phylogenetic software packages.
    http://www.christophheibl.de/Rpackages.html},
  author = {<NAME>},
  year = {2008 onwards},
}

@Book{knitr2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {<NAME>},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@InCollection{knitr2014,
  booktitle = {Implementing Reproducible Computational
    Research},
  editor = {<NAME> and <NAME> and <NAME>},
  title = {knitr: A Comprehensive Tool for Reproducible
    Research in {R}},
  author = {<NAME>},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/
    9781466561595},
}

@Article{muscle2004,
  title = {MUSCLE: multiple sequence alignment with high
    accuracy and high throughput},
  author = {<NAME>},
  year = {2004},
  journal = {Nucleic Acids Res},
  volume = {32},
  pages = {1792-1797},
  doi = {10.1093/nar/gkh340},
}

@Article{phangorn2011,
  title = {phangorn: phylogenetic analysis in R},
  author = {<NAME>},
  journal = {Bioinformatics},
  year = {2011},
  volume = {27},
  number = {4},
  pages = {592--593},
  doi = {10.1093/bioinformatics/btq706},
}

@Article{phangorn2017,
  author = {{Schliep} and {Klaus} and {Potts} and Alastair
    J. and {Morrison} and <NAME>. and {Grimm} and <NAME>.},
  title = {Intertwining phylogenetic trees and networks},
  journal = {Methods in Ecology and Evolution},
  volume = {8},
  number = {10},
  doi = {10.1111/2041-210X.12760},
  pages = {1212--1220},
  keywords = {exploratory data analysis, networks, phangorn,
    R, trees},
  year = {2017},
}

@Book{rmarkdown2018,
  title = {R Markdown: The Definitive Guide},
  author = {<NAME> and <NAME> and <NAME>},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{rmarkdown2020,
  title = {R Markdown Cookbook},
  author = {<NAME> and <NAME> and <NAME>},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@InCollection{seqinr2007,
  author = {<NAME> and <NAME>},
  title = {Seqin{R} 1.0-2: a contributed package to the {R}
    project for statistical computing devoted to biological
    sequences retrieval and analysis.},
  booktitle = {Structural approaches to sequence evolution:
    Molecules, networks, populations},
  year = {2007},
  editor = {<NAME> and <NAME> and <NAME> and <NAME>},
  series = {Biological and Medical Physics, Biomedical
    Engineering},
  pages = {207-232},
  address = {New York},
  publisher = {Springer Verlag},
  note = {{ISBN :} 978-3-540-35305-8},
}

@Article{ShortRead2009,
  title = {{ShortRead}: a {B}ioconductor package for input,
    quality assessment and exploration of high-throughput
    sequence data},
  author = {<NAME> and <NAME> and <NAME> and <NAME> and <NAME> and
    <NAME>},
  year = {2009},
  journal = {Bioinformatics},
  volume = {25},
  pages = {2607-2608},
  doi = {10.1093/bioinformatics/btp450},
  url = {http://dx.doi.org10.1093/bioinformatics/btp450},
}

@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {<NAME> and <NAME> and <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME> and <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME> and
    <NAME> and <NAME> and <NAME>
    and <NAME> and <NAME> and <NAME> and
    <NAME>},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}

