How to cite the Bioconductor package treeio

treeio is a popular Bioconductor package that is available at https://bioconductor.org/packages/treeio. By citing R packages in your paper you lay the grounds for others to be able to reproduce your analysis and secondly you are acknowledging the time and work people have spent creating the package.

APA citation

Formatted according to the APA Publication Manual 7th edition. Simply copy it to the References page as is.

APA

The minimal requirement is to cite the R package in text along with the version number. Additionally, you can include the reference list entry the authors of the treeio package have suggested.

Example of an in-text citation

Analysis of the data was done using the treeio package (v1.14.3; Wang et al., 2020).

Reference list entry

Wang, L.-G., Lam, T. T.-Y., Xu, S., Dai, Z., Zhou, L., Feng, T., Guo, P., Dunn, C. W., Jones, B. R., Bradley, T., Zhu, H., Guan, Y., Jiang, Y., & Yu, G. (2020). Treeio: An R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution, 37(2), 599–603.

Vancouver citation

Formatted according to Vancouver style. Simply copy it to the references section as is.

Vancouver

Example of an in-text citation

Analysis of the data was done using the treeio package v1.14.3 (1).

Reference list entry

1.
Wang LG, Lam TTY, Xu S, Dai Z, Zhou L, Feng T, et al. Treeio: An R package for phylogenetic tree input and output with richly annotated and associated data. Mol Biol Evol. 2020 Feb 1;37(2):599–603.

BibTeX

Reference entry in BibTeX format. Simply copy it to your favorite citation manager.

BibTeX
@ARTICLE{Wang2020-ul,
  title     = "Treeio: An {R} package for phylogenetic tree input and output
               with richly annotated and associated data",
  author    = "Wang, Li-Gen and Lam, Tommy Tsan-Yuk and Xu, Shuangbin and Dai,
               Zehan and Zhou, Lang and Feng, Tingze and Guo, Pingfan and Dunn,
               Casey W and Jones, Bradley R and Bradley, Tyler and Zhu, Huachen
               and Guan, Yi and Jiang, Yong and Yu, Guangchuang",
  abstract  = "Abstract Phylogenetic trees and data are often stored in
               incompatible and inconsistent formats. The outputs of software
               tools that contain trees with analysis findings are often not
               compatible with each other, making it hard to integrate the
               results of different analyses in a comparative study. The treeio
               package is designed to connect phylogenetic tree input and
               output. It supports extracting phylogenetic trees as well as the
               outputs of commonly used analytical software. It can link
               external data to phylogenies and merge tree data obtained from
               different sources, enabling analyses of phylogeny-associated
               data from different disciplines in an evolutionary context.
               Treeio also supports export of a phylogenetic tree with
               heterogeneous-associated data to a single tree file, including
               BEAST compatible NEXUS and jtree formats; these facilitate data
               sharing as well as file format conversion for downstream
               analysis. The treeio package is designed to work with the
               tidytree and ggtree packages. Tree data can be processed using
               the tidy interface with tidytree and visualized by ggtree. The
               treeio package is released within the Bioconductor and rOpenSci
               projects. It is available at
               https://www.bioconductor.org/packages/treeio/.",
  journal   = "Mol. Biol. Evol.",
  publisher = "Oxford University Press (OUP)",
  volume    =  37,
  number    =  2,
  pages     = "599--603",
  month     =  feb,
  year      =  2020,
  url       = "http://dx.doi.org/10.1093/molbev/msz240",
  copyright = "https://academic.oup.com/journals/pages/open\_access/funder\_policies/chorus/standard\_publication\_model",
  language  = "en",
  issn      = "0737-4038, 1537-1719",
  doi       = "10.1093/molbev/msz240"
}

RIS

Reference entry in RIS format. Simply copy it to your favorite citation manager.

RIS
TY  - JOUR
AU  - Wang, Li-Gen
AU  - Lam, Tommy Tsan-Yuk
AU  - Xu, Shuangbin
AU  - Dai, Zehan
AU  - Zhou, Lang
AU  - Feng, Tingze
AU  - Guo, Pingfan
AU  - Dunn, Casey W
AU  - Jones, Bradley R
AU  - Bradley, Tyler
AU  - Zhu, Huachen
AU  - Guan, Yi
AU  - Jiang, Yong
AU  - Yu, Guangchuang
AD  - Department of Bioinformatics, School of Basic Medical Sciences, Southern
      Medical University, Guangzhou, Guangdong, China; State Key Laboratory of
      Emerging Infectious Disease and Centre of Influenza Research, School of
      Public Health, The University of Hong Kong, Hong Kong SAR, China;
      Department of Ecology and Evolutionary Biology, Yale University, New
      Haven, CT; British Columbia Centre for Excellence in HIV/AIDS, Vancouver,
      Canada; Civil, Architectural, and Environmental Engineering, Drexel
      University, Philadelphia, PA; State Key Laboratory of Emerging Infectious
      Disease and Centre of Influenza Research, School of Public Health, The
      University of Hong Kong, Hong Kong SAR, China; Joint Institute of Virology
      (Shantou University – The University of Hong Kong), Shantou University,
      Shantou, Guangdong, China; State Key Laboratory of Emerging Infectious
      Disease (HKU Shenzhen Base), Shenzhen Third People’s Hospital, Shenzhen,
      Guangdong, China; Guangdong Provincial Key Laboratory of Proteomics,
      School of Basic Medical Sciences, Southern Medical University, Guangzhou,
      Guangdong, China; Department of Bioinformatics, School of Basic Medical
      Sciences, Southern Medical University, Guangzhou, Guangdong, China;
      Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical
      Sciences, Southern Medical University, Guangzhou, Guangdong, China
TI  - Treeio: An R package for phylogenetic tree input and output with richly
      annotated and associated data
T2  - Mol. Biol. Evol.
VL  - 37
IS  - 2
SP  - 599-603
PY  - 2020
DA  - 2020/2/1
PB  - Oxford University Press (OUP)
AB  - Abstract Phylogenetic trees and data are often stored in incompatible and
      inconsistent formats. The outputs of software tools that contain trees
      with analysis findings are often not compatible with each other, making it
      hard to integrate the results of different analyses in a comparative
      study. The treeio package is designed to connect phylogenetic tree input
      and output. It supports extracting phylogenetic trees as well as the
      outputs of commonly used analytical software. It can link external data to
      phylogenies and merge tree data obtained from different sources, enabling
      analyses of phylogeny-associated data from different disciplines in an
      evolutionary context. Treeio also supports export of a phylogenetic tree
      with heterogeneous-associated data to a single tree file, including BEAST
      compatible NEXUS and jtree formats; these facilitate data sharing as well
      as file format conversion for downstream analysis. The treeio package is
      designed to work with the tidytree and ggtree packages. Tree data can be
      processed using the tidy interface with tidytree and visualized by ggtree.
      The treeio package is released within the Bioconductor and rOpenSci
      projects. It is available at
      https://www.bioconductor.org/packages/treeio/.
SN  - 0737-4038
DO  - 10.1093/molbev/msz240
UR  - http://dx.doi.org/10.1093/molbev/msz240
ER  - 

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