To cite Rclade in publications, use: Rclade builds on the ggtree and deeptime ecosystems. If you use Rclade in published research, please also cite these key dependencies:

Zeng Z (2026). Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization. R package version 1.1.2.

Yu G, Smith D, Zhu H, Guan Y, Lam T (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8(1), 28-36. doi:10.1111/2041-210X.12628.

Gearty W (2025). “deeptime: an R package that facilitates highly customizable and reproducible visualizations of data over geological time intervals.” Big Earth Data. doi:10.1080/20964471.2025.2537516.

Corresponding BibTeX entries:

  @Manual{,
    title = {Rclade: Automated Deep-Time Phylogenetic Tree Collapsing
      and Visualization},
    author = {Zichao Zeng},
    year = {2026},
    note = {R package version 1.1.2},
  }

  @Article{,
    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},
    number = {1},
    pages = {28-36},
    doi = {10.1111/2041-210X.12628},
  }

  @Article{,
    title = {deeptime: an R package that facilitates highly
      customizable and reproducible visualizations of data over
      geological time intervals},
    author = {William Gearty},
    journal = {Big Earth Data},
    year = {2025},
    doi = {10.1080/20964471.2025.2537516},
  }