The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Open accessAbstract
Summary: We present an r package, ggtree , which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick , nexus , NHX , phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of beast , epa , hyphy , paml , phylodog , pplacer , r8s , raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic‐2.0 license . The source code and documents are freely available through bioconductor ( http://www.bioconductor.org/packages/ggtree ).
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ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447
BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Cited by
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Development of an inactivated vaccine candidate for SARS-CoV-2
Gao, Q., Bao, L., Mao, H., Wang, L., Xu, K., Yang, M., Li, Y., Zhu, L., Wang, N., Lv, Z., et al. (2020) · Science · doi:10.1126/science.abc1932 · Cited by 1,434
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion
Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., Collier, D. A., Albecka, A., Singh, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03944-y · Cited by 1,337
Zeng, D., Li, M., Zhou, R., Zhang, J., Sun, H., Shi, M., Bin, J., Liao, Y., Rao, J., & Liao, W. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0436 · Cited by 986
“R package ggtree (51) was used to visualize phylogenetic trees of the TME signature genes.”
Method
Metadata
- Authors
- Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T.
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2016-09-22
- Volume
- 8
- Issue
- 1
- Pages
- 28-36
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W2513727910
- Cited by
- 4,823
- References
- 3
- FWCI
- 67.71
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. 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. https://doi.org/10.1111/2041-210x.12628
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