Thanks for this great set of tools!
I would like to use the tools for marker gene extraction and alignment without necessarily inferring the genomes’ position on the GTDB tree. Could this be possible (or made possible with a minor change), without needing to download the full gtdbtk_v2_data.tar.gz data?
You will need to download the GTDB-Tk reference data in order to identify the marker genes. Admittedly, all this reference data isn’t required to identify marker genes, but the HMM model files are required. In order to keep installation and software maintenance manageable we don’t want to create different subsets of the reference data.