Bioinformatics with Python Cookbook

Chapter 4. Population Genetics

In this chapter, we will cover the following recipes:

• Managing datasets with PLINK
• Introducing the Genepop format
• Exploring a dataset with Bio.PopGen
• Computing F-statistics
• Performing Principal Components Analysis
• Investigating population structure with Admixture

Introduction

Population genetics is the study of changes of frequency of alleles in a population on the basis of selection, drift, mutation, and migration. The previous chapters focused mainly on data processing and cleanup; this is the first chapter in which we will actually infer interesting biological results.

There is a lot of interesting population genetics analysis based on sequence data, but as we already have quite a few recipes to deal with sequence data, ...