zol: prepTG Databases for ESKAPE Pathogens

Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for one of the six genera containing ESKAPE pathogens. Representative genomes for each genus/taxon were selected using skDER v1.0.7 in greedy mode with 99% ANI and 90% AF cutoffs.

The compressed folders also contain an extra file, corresponding to a species tree of the representative genomes constructed using GToTree with Universal markers (ribosomal proteins) from Hug et al. 2016 and in best-hits mode. Note, GToTree was modified to always use -super5 mode for SCG alignments for computational efficiency. Also, note, because genomes can be dropped by GToTree prior to phylogeny inference (e.g. if they lack enough SCGs), not all genomes in the database might be represented in the phylogenies.