This recipe needs the msa package. This is a pretty hefty package and includes external software: Clustal, Clustal Omega, and Muscle. The ape and seqinR packages are also needed. As a test dataset, we'll use some haemoglobin protein sequences stored in the book's data and code repository at datasets/ch3/hglobin.fa. You'll need PDFLatex on your system too. You can find installation information here: https://www.latex-project.org/get/.