Table 5. CPU runtime of each algorithm in hours.

CVTree and FFP were the fastest algorithms. CAM and Amino acid motifs had comparable runtimes and were faster than ACS, andi, FSWM, and maximum likelihood.

Taxonomic group	CAM	Amino acid motifs	FFP	CVTree	ACS	Andi	FSWM	Maximum likelihood
All	17.2794	20.2692	3.9072	N/A	N/A	N/A	N/A	N/A
Archaea	0.0667	0.1436	0.0408	0.0236	28.87	8.05	28.83	161.5
Bacteria	14.6994	17.4458	3.7442	N/A	N/A	N/A	N/A	N/A
Fungi	0.0783	0.2167	0.0294	0.0028	42.12	8.75	56.92	199.75
Invertebrates	0.0763	0.2126	0.0447	0.0150	28.75	5.88	54.93	2.5
Plants	0.0781	0.2211	0.0383	0.0217	22.17	4.21	49.77	6.0
Protozoa	0.0287	0.0833	0.0183	0.0078	4.88	1.01	20.65	4.0
Mammals	0.0718	0.2101	0.0294	0.0122	22.32	4.32	63.25	2.5
Other vertebrates	0.0872	0.2356	0.0322	0.0206	27.03	5.63	61.35	6.75
Viruses	0.1028	0.1161	0.1019	0.2906	42.53	12.67	6.03	N/A