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, we will divert our attention somewhere else. Also, we will not cover genomic structural variation such as Copy Number Variation (CNVs) or inversions here. I will concentrate on analyzing SNP data, which is one of the most common. We will perform many standard analyses, including population genetic analyses with Python, such as F_ST (Fixation index), Principal Components Analysis (PCA), and study of population structure.

We will use Python as a scripting language that glues together applications that perform necessary computations...