Table 1. Percentage of bases correctly assigned to modeled taxa by different methods for the AMD metagenome scaffolds.

Rank	PhyloPythiaS sample-specific	PhyloPythiaS generic	BLASTN	MEGAN	NBC
Genus	41.353	0.000	0.000	0.000	0.000
Family	41.353	0.000	1.685	0.000	0.000
Order	74.706	38.189	45.536	42.210	1.742
Class	74.706	38.189	45.536	42.210	1.742
Phylum	89.540	47.821	47.011	42.673	1.798
Domain	92.673	88.978	86.042	70.194	44.805

The reference taxonomic affiliations were obtained by aligning the test scaffolds with the draft genomes. For PhyloPythiaS (both generic and sample-specific), the drop in accuracy is mostly due to unassigned sequences at a particular rank, while other methods produced more false assignments. Thermoplasmatales archaeon Gpl (comprising 21.8% of the total bases) has no defined parental clade at the genus and family ranks, contributing to the observed lower accuracy values for these ranks. Additional measures are shown in Figure S6.