Can I get ID's for the actual strains from strainphlan?

Microbial community profiling StrainPhlAn
1

I have run metaphlan and strainphlan on my samples following the tutorial. It all seems to have worked, however when I visualise the output RAxML_bestTree.t__SGB7852.StrainPhlAn4.tre file there is no ID on what strains are present, the branches just differentiate by the sample name.

Is it possible to get the actual strain names from strainphlan?

2

Hi @mradz19
Sorry for the misundertanding, StrainPhlan do not report strain IDs but builds strain-level phylogenies using the reconstructed consensus sequences directly from the metagenomic reads.