How to identify lineages from whole genome assemblies

Question

[ddh8602]

Hi everyone, I have aroung 60 whole genomes assemblies from L. monocytogenes and I am wondering if there is an easy way to designate the lineage to each genome. I know I can build a phylogenetic tree and try to group branches into lineages but how do I know which one falls into each group ? Is there a standard way of doing it ?

[juanjo75es]

I guess there is no standard way to do that and that's why phylogenetic trees are still a thing. If there were another way we would not use these. As you likely know, phylogenetic trees have some limitations.