Table 1. Details of TQMD runs and phylogenomic datasets built on eight different subsets of Bacteria.

For each dataset, TQMD was launched with the Jaccard Index as a distance, a pack size of 200, the loose clustering mode, and was allocated a maximum of 50 CPUs. Other parameters (direct or indirect strategy and distance threshold) are provided in the table, along with the total running time in CPU hours (h.CPU), the initial number of genomes (# starting), the number of representatives obtained (# repr.), the number of ribosomal protein alignments used in the supermatrix (# prot.), and the number of unambiguously aligned amino acids in the supermatrix (# AA). Further details (taxonomy and download links, Krona taxonomic plots, Forty-Two reports, supermatrices and trees) are available at https://doi.org/10.6084/m9.figshare.13238936.

Label	Dataset	Strategy	Threshold	h.CPU	# starting	# repr.	# prot.	# AA
A	Bacteria (49)	indirect	0.900	656	63,863	49	53	6338
B	Bacteria (151)	indirect	0.880	656	63,863	151	53	6187
C	Actinobacteria	direct	0.900	96	8859	20	51	6562
D	Bacteroidetes	direct	0.850	16	1225	37	49	6605
E	Chlamydia	direct	0.800	6	360	32	44	6131
F	Cyanobacteria	direct	0.800	8	428	46	48	6314
G	Firmicutes	direct	0.900	242	21,544	22	52	6536
H	Proteobacteria	direct	0.885	310	30,690	36	53	6471
I	Archaea	direct	0.850	8	432	86	57	7810