Literatura
Visualización y anotación de árboles
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T.-Y. (2017). ggtree… Methods in Ecology and Evolution, 8(1), 28–36. DOI: 10.1111/2041-210X.12628.
Yu, G. (2020). Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 69(1), e96. DOI: 10.1002/cpbi.96.
Wang, L.-G., Lam, T. T.-Y., Xu, S., et al. (2020). treeio: An R package for phylogenetic tree input and output… Molecular Biology and Evolution, 37(2), 599–603. DOI: 10.1093/molbev/msz240.
Paradis, E., & Schliep, K. (2019). ape 5.0… Bioinformatics, 35(3), 526–528. DOI: 10.1093/bioinformatics/bty633.
Yu, G. (2022/2023). Data Integration, Manipulation and Visualization of Phylogenetic Trees. Chapman & Hall/CRC. Sitio del libro en línea.
Inferencia filogenética (para contextualizar las figuras)
Alfaro, M. E., & Holder, M. T. (2006). The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 37, 19–42. DOI: 10.1146/annurev.ecolsys.37.091305.110021.
Alfaro, M. E., Zoller, S., & Lutzoni, F. (2003). Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence. Molecular Biology and Evolution, 20(2), 255–266. DOI: 10.1093/molbev/msg028.
Minh, B. Q., Schmidt, H. A., Chernomor, O., et al. (2020). IQ-TREE 2… Molecular Biology and Evolution, 37(5), 1530–1534. DOI: 10.1093/molbev/msaa015.
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG… Bioinformatics, 35(21), 4453–4455. DOI: 10.1093/bioinformatics/btz305.
Ronquist, F., Teslenko, M., van der Mark, P., et al. (2012). MrBayes 3.2… Systematic Biology, 61(3), 539–542. DOI: 10.1093/sysbio/sys029.
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., et al. (2019). BEAST 2.5… PLOS Computational Biology, 15(4), e1006650. DOI: 10.1371/journal.pcbi.1006650.
Höhna, S., Landis, M. J., Heath, T. A., et al. (2016). RevBayes… Systematic Biology, 65(4), 726–736. DOI: 10.1093/sysbio/syw021.
Gráficos en R y bases para figuras reproducibles
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis (2ª ed.). Springer. DOI: 10.1007/978-3-319-24277-4.
Wickham, H., Averick, M., Bryan, J., et al. (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686. DOI: 10.21105/joss.01686.
Reproducibilidad y redacción (R Markdown)
Xie, Y., Allaire, J. J., & Grolemund, G. (2018). R Markdown: The Definitive Guide. CRC Press. En línea: Bookdown
Markdown Guide. (s.f.). Markdown Cheat Sheet. Disponible en: markdownguide.org/cheat-sheet.