Table 3.

Comparison of the taxonomic classification accuracy of the different BLASTx-based methods CARMA3_BLASTx, SOrt-ITEMS and MEGAN

	Order-filtered						Species-filtered						All
	CARMA3		SOrt-ITEMS		MEGAN		CARMA3		SOrt-ITEMS		MEGAN		CARMA3		SOrt-ITEMS		MEGAN
	TP	FP	TP	FP	TP	FP	TP	FP	TP	FP	TP	FP	TP	FP	TP	FP	TP	FP
Superkingdom	12696	861	12576	786	12626	1849	20266	118	20345	128	20840	453	22890	36	23979	30	23900	105
Phylum	8989	1224	9254	1736	8079	1985	19268	227	19466	356	19010	535	22832	30	23909	43	23607	91
Class	4066	1495	4062	1937	3649	2479	16206	349	16259	401	15921	735	20932	38	21912	41	21418	107
Order	–	2507	–	4011	–	4975	15671	366	15684	535	15105	954	21994	65	22871	58	21543	155
Family	–	1186	–	2565	–	4087	12117	345	13104	606	11625	1101	20089	62	20864	59	18937	143
Genus	–	210	–	798	–	4041	8328	752	8299	1112	8031	1889	20430	314	21124	483	17758	263
Species	–	23	–	0	–	3544	–	995	–	0	–	4346	15232	685	0	0	11786	550

In the table CARMA3 refers to the BLAST variant CARMA3_BLASTx.