Table 1.

General and BUSCO benchmark statistics for homology grouping performed under setting D1 to D8

Clustering setting	Minimum sequence similarity	Homology groups	Single copy groups	Correct groups a	True Positives	False Positives	False Negatives	Recall	Precision	F-score
D1	95%	49,290	812	395	128,085	14	3905	0.9704	0.9999	0.9849
D2	85%	28,896	1615	629	131,795	24	195	0.9985	0.9998	0.9992
D3	75%	24,650	1690	638	131,952	35	38	0.9997	0.9997	0.9997
D4	65%	22,347	1699	640	131,975	38	15	0.9999	0.9997	0.9998
D5	55%	20,636	1683	639	131,975	44	15	0.9999	0.9997	0.9998
D6	45%	19,234	1653	633	131,985	245	5	0.9981	0.9981	0.9991
D7	35%	17,908	1612	623	131,985	508	5	0.9962	0.9962	0.9981
D8	25%	16,486	1486	607	131,986	7002	4	1.0000	0.9496	0.9741

^a Correct groups are defined as the number of groups that correctly organize one out of 670 ‘complete’ and ‘non-duplicated’ Enterobacteriaceae BUSCO genes. Calculations of recall, precision, and F-score explained in Methods