Introduction

Population genetics is the study of the 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 for dealing with sequence data, we will divert our attention somewhere else. Also, we will not cover genomic structural variation such as copy number variations (CNVs) or inversions here. We will concentrate on analyzing SNP data, which is one of the most common data types. We will perform many standard population genetic analyses with Python, such as fixation index (F_ST) with computing F-statistics, Principal Components Analysis (PCA), and study population structure.

We will use Python mostly as a scripting language that glues together applications that...