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.

Hartman et al. BMC Bioinformatics 2010 11:317   doi:10.1186/1471-2105-11-317

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