Table 1.

Comparison of WATERS' tools to existing web services and stand-alone software tools.

	Greengenes	RDP II	RDP-Py	Silva	Mothur	QIIME	WATERS
Use	Web	Web	Web	Web	Command line	Command line	GUI
Align	NAST	Infernal	Infernal	SINA	NAST		Infernal
Chimeras	Bellerohpon	No	No	No	Unknown		Mallard
OTUs	Yes	DOTUR	Complete-linkage	No	DOTUR		OTUHunter
Taxonomy	Simrank; 7mer classification	naïve Bayesian classifier	naïve Bayesian classifier	Yes	Yes		STAP
Trees	No	NJ	NJ	No	Yes		ML; NJ
Ecology	No	No	Yes	No	Yes		Yes
Unifrac	No	No	No	No	Yes		Yes
Export	Yes	Yes	No	Yes	No		No
Trim?	Yes	Yes	Yes	No	Yes		No
Data size?	hundreds	hundreds	500,000	hundreds	tens of thousands	tens of thousands	tens of thousands

Along the left column, "Use" indicates where or how the software is used; "Align" indicates the alignment programs available; "Chimeras" indicates the chimera removal software available; "OTUs" indicates the software used to detect and determine operational taxonomic units; "Taxonomy" indicates the software used to assign taxonomy to OTUs; "Trees" indicates the software used to build phylogenetic trees; "Ecology" indicates whether or not ecological indices such as Chao1 and the Shannon index are calculated; "Unifrac" indicates whether Unifrac analyses are done within the software or whether data is formatted for downstream use in Unifrac; "Export DB" indicates whether a quality-controlled, curated 16 S dataset is available for export and/or for comparison to the user's own dataset; "Trim" indicates the availability of quality control trimming to remove sequence vectors or low-quality bases from the initial upload of sequences; "Dataset size" indicates the estimated amount of sequences that can be readily processed through each software type. Along the top are all known multi-tool 16 S rDNA analysis software suites. Note that these software are each under very active development. This table represents a snapshot in time of current tool availabilities. ML, maximum-likelihood; NJ, neighbor-joining.