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
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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
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