@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Lionel Henry},
  year = {2020},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=tidyr},
}
@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 = {2019},
  url = {https://www.R-project.org/},
}
@Manual{R-crayon,
  title = {crayon: Colored Terminal Output},
  author = {Gábor Csárdi},
  year = {2017},
  note = {R package version 1.3.4},
  url = {https://CRAN.R-project.org/package=crayon},
}
@Manual{R-devtools,
  title = {devtools: Tools to Make Developing R Packages Easier},
  author = {Hadley Wickham and Jim Hester and Winston Chang},
  year = {2019},
  note = {R package version 2.2.1},
  url = {https://CRAN.R-project.org/package=devtools},
}
@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2019},
  note = {R package version 0.8.3},
  url = {https://CRAN.R-project.org/package=dplyr},
}
@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  note = {R package version 3.2.1},
  url = {https://CRAN.R-project.org/package=ggplot2},
}
@Manual{R-ggpubr,
  title = {ggpubr: 'ggplot2' Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2019},
  note = {R package version 0.2.3},
  url = {https://CRAN.R-project.org/package=ggpubr},
}
@Manual{R-ggtree,
  title = {ggtree: an R package for visualization and annotation of phylogenetic
trees with their covariates and other associated data},
  author = {Guangchuang Yu and Tommy Tsan-Yuk Lam},
  year = {2019},
  note = {R package version 1.16.6},
  url = {https://yulab-smu.github.io/treedata-book/},
}
@Manual{R-phytools,
  title = {phytools: Phylogenetic Tools for Comparative Biology (and Other Things)},
  author = {Liam J. Revell},
  year = {2019},
  note = {R package version 0.6-99},
  url = {https://CRAN.R-project.org/package=phytools},
}
@Manual{R-plyr,
  title = {plyr: Tools for Splitting, Applying and Combining Data},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.8.5},
  url = {https://CRAN.R-project.org/package=plyr},
}
@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}
@Article{ggtree2017,
  title = {ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.},
  author = {Guangchuang Yu and David Smith and Huachen Zhu and Yi Guan and Tommy Tsan-Yuk Lam},
  year = {2017},
  journal = {Methods in Ecology and Evolution},
  volume = {8},
  issue = {1},
  pages = {28-36},
  doi = {10.1111/2041-210X.12628},
  url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
}
@Article{ggtree2018,
  title = {Two methods for mapping and visualizing associated data on phylogeny using ggtree.},
  author = {Guangchuang Yu and Tommy Tsan-Yuk Lam and Huachen Zhu and Yi Guan},
  year = {2018},
  journal = {Molecular Biology and Evolution},
  volume = {35},
  issue = {2},
  pages = {3041-3043},
  doi = {10.1093/molbev/msy194},
  url = {https://doi.org/10.1093/molbev/msy194},
}
@Article{phytools2012,
  title = {phytools: An R package for phylogenetic comparative biology (and other things).},
  author = {Liam J. Revell},
  journal = {Methods in Ecology and Evolution},
  year = {2012},
  volume = {3},
  pages = {217-223},
  url = {https://doi.org/10.1111/j.2041-210X.2011.00169.x}
}
@Article{plyr2011,
  title = {The Split-Apply-Combine Strategy for Data Analysis},
  author = {Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {1},
  pages = {1--29},
  url = {https://www.jstatsoft.org/article/view/v040i01},
}
@Article{rentrez2017,
  title = {{rentrez}: an R package for the NCBI eUtils API},
  author = {David J. Winter},
  journal = {The R Journal},
  year = {2017},
  volume = {9},
  issue = {2},
  pages = {520--526},
}
@Manual{Roa2021,
  title = {{idiogramFISH}: Shiny app. {I}diograms with Marks and Karyotype Indices},
  author = {Fernando Roa and Mariana {PC Telles}},
  organization = {Universidade Federal de Goiás},
  address = {UFG, Goiânia},
  note = {R-package. version 2.0.0},
  year = {2021},
  url = {https://ferroao.gitlab.io/manualidiogramfish/},
  doi = {10.5281/zenodo.3579417},
}
@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
  year = {2020},
  note = {http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2},
}

@Manual{R-reshape2,
  title = {reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.4.4},
  url = {https://CRAN.R-project.org/package=reshape2},
}

@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}

@Article{reshape22007,
  title = {Reshaping Data with the {reshape} Package},
  author = {Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {21},
  number = {12},
  pages = {1--20},
  url = {http://www.jstatsoft.org/v21/i12/},
}

