This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole genome/core-genome phylogeny?
For instace, I am drawing a core-genome phylogeny of Staphylococcus aureus genomes taken from NCBI as well as from my own sequenced ones. Now, my isolates have grouped with several isolates from NCBI (Bottom four greens with four red ones). I want to know, weather these isolates are actually closely related to NCBI ones or they are just those strains themselves?
Thank you all in advance!