This recipe requires RAxML, a program for maximum likelihood-based inference of large phylogenetic trees, which you can check out at http://sco.h-its.org/exelixis/software.html. Bioconda includes it, where it is named raxml. Note that the binary is called raxmlHPC.
The code here is simple, but it will take time to execute because it will call RAxML (which is computationally intensive). If you opt to use the DendroPy interface, it may also become memory-intensive. We will interact with RAxML, DendroPy, and Biopython, leaving you with a choice of which interface to use; DendroPy gives you an easy way to access results, whereas Biopython is less memory-intensive. Although there is a recipe for visualization later in this chapter, ...
