Reconstructing phylogenetic trees

Here, we will construct phylogenetic trees for the aligned dataset for all Ebola species. We will follow a procedure that’s quite similar to the one used in the paper.

Getting ready

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 also includes it, but it is named raxml. Note that the binary is called raxmlHPC. You can perform the following command to install it:

conda install –c bioconda raxml

The preceding code 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 might 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...