Bioinformatics with Python Cookbook

Reconstructing phylogenetic trees

Here, we will construct phylogenetic trees for the aligned dataset for all Ebola species. We will follow the procedure 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 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 ...