O'Reilly logo

Bioinformatics with Python Cookbook by Tiago Antao

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

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 ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required