I am new to the world of population statistics and need some help!

I have a collection of very closely related strains of the same species of bacteria (average 10 SNPs apart) and want to understand if any of these SNPs are under selection.

I am trying to figure out the best way to calculate Pn/Ps for a whole genome alignment? I have both the alignment and SNP data (VCF and Snpeff annotations) for each strain relative to a reference if that is helpful.

I am really looking for an easy program that allows me to just input the alignment and runs the appropriate stats. But I am not sure if that exists or not.