Table 6. Runtime (h) of the ML methods on the six smallest biological datasets.

Alignment	Method	16S.M.aa_ag	16S.M	23S.M	23S.M.aa_ag	23S.E.aa_ag	23S.E	Average
Reference	RAxML	7.54	5.90	2.33	2.25	0.99	0.78	3.30
	FastTree	0.08	0.06	0.04	0.03	0.02	0.02	0.04
	RAxML-Limited	0.24	0.22	0.10	0.10	0.04	0.03	0.12
SATé	RAxML	6.26	4.51	1.57	1.37	0.67	0.62	2.50
	FastTree	0.14	0.06	0.03	0.03	0.02	0.02	0.05
	RAxML-Limited	0.21	0.18	0.07	0.07	0.03	0.03	0.10
MAFFT	RAxML	4.27	3.99	1.56	2.28	0.88	0.53	2.25
	FastTree	0.07	0.06	0.03	0.03	0.02	0.01	0.04
	RAxML-Limited	0.16	0.16	0.08	0.29	0.03	0.03	0.12
PartTree	RAxML	10.05	7.19	2.71	1.86	0.85	0.76	3.90
	FastTree	0.16	0.11	0.05	0.08	0.02	0.02	0.07
	RAxML-Limited	0.33	0.28	0.09	0.08	0.03	0.03	0.14
ClustalW	RAxML	5.99	3.73	1.64	2.10	0.66	0.51	2.44
	FastTree	0.05	0.04	0.02	0.02	0.01	0.01	0.03
	RAxML-Limited	0.14	0.11	0.06	0.06	0.02	0.02	0.07
Quicktree	RAxML	5.46	3.37	1.48	1.38	0.90	0.58	2.19
	FastTree	0.05	0.04	0.02	0.02	0.01	0.01	0.03
	RAxML-Limited	0.19	0.12	0.05	0.05	0.03	0.02	0.08

“Average” refers to the average across the datasets. n = 1 for values in columns other than the “Average” column. n = 6 for the “Average” column.