Protal is a computational tool for taxonomic profiling and strain-resolved analyses of bacterial communities from metagenomic shotgun sequencing data (short-reads). Following a reference-based approach, protal uses the same 120 universal marker genes GTDB uses to build their phylogeny (TIGRFAM, PFAM) and thus integrates well with other 120 universal marker genes GTDB uses to build their phylogeny (TIGRFAM, PFAM) and thus integrates well with other tools working in the GTDB taxonomy space.