I have run the classify_wf command on my 140 MAGs (Clostridium species). I have obtained the “gtdbtk.bac120.classify.tree.2.tree” file and I have converted this last in itol format with the convert_to_itol command
I have put this file in itol website in “upload a tree” section, I can auto assign the taxonomy for GTDB but not for NCBI
So for the next step, I would like now just convert this gtdbtk itol tree into ncbi itol tree for all the taxonomy (all Bacteria, not just my MAGs) and watch where my MAGs are placed among other strains in NCBI taxonomy. I know that the taxonomy between NCBI and GTDBTK is not a 1:1 match, but is it possible ?