Population-genomics-analysis

This repository contains various analysis scripts for analysis of microbial population genomics -- a valuable tool to define and delimit species and to understand the mechanisms that drive and maintain speciation.

The following modules were employed in this study:

1. SNP density plot

2. Recombination inference

3. Population structure inference

4. Recombined genes inference based on pairwise dS values

You may need to learn about some commonly used software in population genomics analysis before utilizing these scripts:

fineStructure

ClonalFrameML

Mauve