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:
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SNP density plot
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Recombination inference
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Population structure inference
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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: