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.
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.
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.
@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.
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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