Table 2.

Taxonomic assignment performance (%) and speed of HmmUFOtu and two similar tools, pplacer and EPA, at different taxonomy levels

Dataset		Performance measurement							Speed
		Kingdom	Phylum	Class	Order	Family	Genus	Species
Random	TPR	100.00	99.96	99.52	99.22	98.87	95.03	81.96	3.14
	TNR	nan	96.98	91.76	96.04	98.09	98.09	99.35
	PPV	100.00	99.99	99.63	99.43	99.10	95.94	84.85
	ACC	100.00	99.94	99.19	98.82	98.62	97.10	98.62
V4	TPR	100.00	99.96	99.52	99.26	99.17	95.78	82.75	4.61
	TNR	nan	94.85	91.17	95.93	97.98	98.17	99.44
	PPV	100.00	99.98	99.60	99.41	99.06	96.09	86.10
	ACC	100.00	99.94	99.15	98.84	98.79	97.40	98.77
V1 V3	TPR	100.00	99.97	99.45	99.18	98.93	95.34	82.89	3.22
	TNR	nan	98.84	89.52	95.51	97.56	97.93	99.26
	PPV	100.00	99.99	99.51	99.36	98.86	95.53	82.83
	ACC	100.00	99.96	99.01	98.72	98.49	97.11	98.58
V3 V5	TPR	100.00	99.96	99.61	99.39	99.40	96.98	86.71	3.15
	TNR	nan	98.17	94.86	97.73	99.17	98.97	99.64
	PPV	100.00	99.99	99.77	99.68	99.61	97.78	91.05
	ACC	100.00	99.96	99.41	99.18	99.33	98.34	99.12
Program		Performance measurement							Speed
		Kingdom	Phylum	Class	Order	Family	Genus	Species
HmmUFOtu	TPR	100.00	98.36	95.60	91.63	86.72	83.31	84.02	12.02
	TNR	nan	95.05	94.97	96.29	97.50	98.71	99.71
	PPV	100.00	99.11	95.65	90.81	84.11	80.48	83.04
	ACC	100.00	97.86	95.31	94.96	96.07	97.79	99.44
Pplacer	TPR	100.00	99.92	99.68	99.58	99.70	100.00	100.00	3.23
	TNR	nan	69.13	74.95	80.48	87.40	93.56	98.12
	PPV	100.00	94.77	82.16	67.11	54.72	49.75	47.74
	ACC	100.00	95.25	88.22	85.94	89.03	93.95	98.15
EPA	TPR	100.00	99.52	98.58	98.14	97.89	98.00	97.04	0.27
	TNR	nan	82.12	84.06	87.74	92.06	95.76	98.89
	PPV	100.00	96.89	87.74	76.20	65.31	59.53	60.07
	ACC	100.00	96.88	91.85	90.71	92.83	95.89	98.86

TPR sensitivity, TNR specificity, PPV precision, ACC accuracy, Nan no observed data

Speed is measured as reads per second per processor. Upper panel: results from running HmmUFOtu on four simulated datasets based on gg_97_otus_GTR database; Lower panel: results from running the three tested programs on the random79 dataset based on gg_79_otus_GTR database. Speed is measured as reads per second per processor. Performance measurement results are based on the aggregate of any replicate samples; speed results are based on the average of any replicate samples