Hi @Jeffrey_Chiu
Your are right, the longer the branch length between two strains, the more different the strains are. If you are interested in ways to visualize your data for interpretation, in our tutorial we proposed several options: StrainPhlAn3 · biobakery/biobakery Wiki · GitHub
If you are interested on identify similar strains, you can take a look on this thread: Strain Identity Cutoff - #5 by aitor.blancomiguez
Best,
Aitor