Table 4.

Comparison of pairwise distance-based classification approaches of this study, the standard tool at NCBI, and other studies^a

Aspect	Parameter for indicated classification approach
	DEmARC M-2010	PASC	Others
Genome regions included	All family-wide conserved proteins	Complete genomes	Single genes/proteins, their combinations
Sequence type	aa	nt	aa and/or nt
Alignment	Multiple	Pairwise	Multiple, pairwise
Distance measure	Corrected	Uncorrected	Uncorrected, corrected
No. of taxonomic levels	Data derived	A priori defined	A priori defined
Threshold determinationb	Objective	Subjective	Subjective

^aClassifications are indicated as follows: DEmARC M-2010, this study; PASC, the standard tool at NCBI; others, other studies.

^bIt is indicated how thresholds for partitioning of the distance distribution are determined: using either an objective, data-driven approach (objective) or other means, including rough, subjective placement and missing description (subjective).