Table 4. Overview of how the different classes are predicted, when using the two-step method.

Notice that the frequency of correctly predicted facultative anaerobes have not increased compared with the one-step method (33% vs. 35%), but that the fraction of erroneous predictions of aerobe and anaerobe bacteria have been decreased (5% vs. 11% for aerobes, 4% vs. 6% for anaerobes). Thus the better performance of the prediction of facultative anaerobe genomes is due to an increased accuracy in predicting aerobe and anaerobe bacteria rather than an increased accuracy in predicting facultative anaerobe bacteria.

	Aerobe genomes				Anaerobe genomes				Facultative genomes
Predictions	Aerobe	141	90	%	Aerobe	8	7	%	Aerobe	47	48	%
	Anaerobe	8	5	%	Anaerobe	96	89	%	Anaerobe	18	19	%
	Facultative	8	5	%	Facultative	4	4	%	Facultative	32	33	%