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Table 1 Comparison of WATERS' tools to existing web services and stand-alone software tools.

From: Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

  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
  1. 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.