This recipe requires RAxML, a program for maximum likelihood-based inference of large phylogenetic trees, which you can check at http://sco.h-its.org/exelixis/software.html. With Ubuntu Linux, you can simply apt-get install 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 via DendroPy and Biopython, leaving you with a choice of which interface to use; DendroPy gives an easy way to access results, whereas Biopython is less memory-intensive. Although there is a recipe for visualization later in this chapter, we will nonetheless plot one of our generated trees here...