Table 1.

The initial number of rRNA sequences and the number of sequences excluded for different reasons.

Kingdom	Type	Initial count	Environmental samples	Incomplete sequences	Redundancy reduction	Total in HMM
Archaea	5S	58	0	0	10	48
	16S	589	239	471	287	76
	23S	37	0	18	8	15
Bacteria	5S	461	0	0	101	360
	16S	12 107	1429	10 723	2485	743
	23S	398	0	155	130	127
Eukaryotes	5S	316	0	0	33	283
	18S	6585	24	5222	836	979
	28S	157	0	91	8	58

Environmental samples were excluded due to lack of phylogenetic information. Sequences with too many unknown nucleotides in either end of the sequence were excluded to improve HMM accuracy. Redundancy reduction was performed to reduce bias. Note that these groups may overlap. The last column indicates the number of sequences used to build each HMM.