Entering edit mode
4.1 years ago
Fid_o
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40
I have 900 assembled Salmonella Typhimurium ST313 sequences (.FASTA files, average sequence size 4.7MB). Basic information says there are two lineages of salmonella strains - one an old lineage and another a newer one. The newer one has 22 SNP differences from the old one.
I need to separate which ones are the newer strains and which ones are the older ones. How do I get around this?
Am working from Linux.
try quantTB tool, its basically for TB strains but you can build your own database as well