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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Simulating the coalescent with Biopython and fastsimcoal
While there is a native Python coalescent simulator called CoaSim, this is a very old application that does not run on modern Python versions. As such, if you want to do coalescent simulations with Python, Biopython offers a wrapper to fastsimcoal and the older simcoal.
Here, we will generate some configuration files for fastsimcoal with the demographic and genomic information. We will also run the coalescent simulator from Python.
Getting ready
You will need to obtain fastsimcoal from http://cmpg.unibe.ch/software/fastsimcoal2/. If you are using the Docker image, this is taken care of for you.
If you are using notebooks, this content is in 04_PopSim/Coalescent.ipynb.
How to do it…
Take a look ...
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