The sample data you'll need is available from this book's GitHub repository at https://github.com/danmaclean/R_Bioinformatics_Cookbook. If you want to use the code examples as they are written, then you will need to make sure that this data is located in a subdirectory of whatever your working directory is.
Here are the R packages that you'll need. The majority of these will install with install.packages(); others are a little more complicated:
- ape
- adegraphics
- Bioconductor:
- Biostrings
- ggtree
- treeio
- msa
- devtools
- dotplot
- ggplot2
- phangorn
- treespace
Bioconductor is huge and has its own installation manager. You can install it with the following code:
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install()
