Hi @Dario
Thanks for getting in touch. For identify well-known strains in your samples you first need to include them as reference genomes when calling StrainPhlAn (using the -r / --references parameter). Once StrainPhlAn generates the tree, you can check whether the strains you included are also present in your samples by checking their phylogenetic distance in the tree. Please, see this last post: Strain Identity Cutoff