Bioinformatics with Python Cookbook

Simulating population structure using island and stepping-stone models

We will now simulate population structure. Let's start with an island model and then create a one-dimensional stepping-stone model. We will also study F_ST and distinguish between deme-level statistics and meta-population level statistics. Strictly speaking, we will simulate fragmentation models by splitting into islands or stepping-stones.

Getting ready

Read the first recipe (Introducing forward-time simulations) as it introduces the basic programming framework. If you are using notebooks, the content is in 04_PopSim/Pop_Structure.ipynb.

How to do it…

Take a look at the following steps:

1. Let's start with some basic code from the first recipe:

   from __future__ import division from collections ...