June 2015
Intermediate to advanced
306 pages
6h 50m
English
Content preview from Bioinformatics with Python CookbookBecome an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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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 ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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