To cite ggtree in publications use:

  Guangchuang Yu. (2022). Data Integration, Manipulation and
  Visualization of Phylogenetic Trees (1st edition). Chapman and
  Hall/CRC. doi:10.1201/9781003279242

A BibTeX entry for LaTeX users is

  @Book{,
    title = {Data Integration, Manipulation and Visualization of Phylogenetic Treess},
    author = {Guangchuang Yu},
    publisher = {Chapman and Hall/{CRC}},
    year = {2022},
    edition = {1st edition},
    doi = {10.1201/9781003279242},
    url = {https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/},
  }

  Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan,
  Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A
  serialized data object for visualization of a phylogenetic tree and
  annotation data. iMeta 2022, 4(1):e56. doi:10.1002/imt2.56

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data},
    author = {Shuangbin Xu and Lin Li and Xiao Luo and Meijun Chen and Wenli Tang and Li Zhan and Zehan Dai and {Tommy T. Lam} and Yi Guan and Guangchuang Yu},
    year = {2022},
    journal = {iMeta},
    volume = {1},
    number = {4},
    pages = {e56},
    doi = {10.1002/imt2.56},
    url = {https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56},
  }

  Guangchuang Yu. Using ggtree to visualize data on tree-like
  structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:
  10.1002/cpbi.96

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Using ggtree to Visualize Data on Tree-Like Structures},
    author = {Guangchuang Yu},
    year = {2020},
    journal = {Current Protocols in Bioinformatics},
    volume = {69},
    pages = {e96},
    number = {1},
    url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96},
    doi = {10.1002/cpbi.96},
  }

  Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods
  for mapping and visualizing associated data on phylogeny using
  ggtree. Molecular Biology and Evolution 2018, 35(2):3041-3043. doi:
  10.1093/molbev/msy194

A BibTeX entry for LaTeX users is

  @Article{,
    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://academic.oup.com/mbe/article/35/12/3041/5142656},
  }

  Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk
  Lam. ggtree: an R package for visualization and annotation of
  phylogenetic trees with their covariates and other associated data.
  Methods in Ecology and Evolution 2017, 8(1):28-36.
  doi:10.1111/2041-210X.12628

A BibTeX entry for LaTeX users is

  @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},
    issue = {1},
    pages = {28-36},
    doi = {10.1111/2041-210X.12628},
    url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
  }