SNP Bacterial Genomes per year
 

I am looking at SNP trees for bacterial genomes (mostly N. gonorrhoeae, S. aureus and E. faecium) and I am following outbreaks in society and on hospital wards.
Do you know the number of SNPs that will appear per year for the different species, and where I can find some information about that.
Best Regards
Peder Worning

You want probably want to use snpRelate for this, seeing as you only have the vcfs.

But, hypothetically there are tools that will let you turn vcf +reference files to a contig so the process is Vcfs->fastas(the contigs for all vcfs)-mafft(an multiple sequence aligner)> msa.fa -phyml-> phylogenetic tree