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 | Â | Infernal |
Chimeras | Bellerohpon | No | No | No | Unknown | Â | Mallard |
OTUs | Yes | DOTUR | Complete-linkage | No | DOTUR | Â | OTUHunter |
Taxonomy | Simrank; 7mer classification | naïve Bayesian classifier | naïve Bayesian classifier | Yes | Yes |  | STAP |
Trees | No | NJ | NJ | No | Yes | Â | ML; NJ |
Ecology | No | No | Yes | No | Yes | Â | Yes |
Unifrac | No | No | No | No | Yes | Â | Yes |
Export | Yes | Yes | No | Yes | No | Â | No |
Trim? | Yes | Yes | Yes | No | Yes | Â | No |
Data size? | hundreds | hundreds | 500,000 | hundreds | tens of thousands | tens of thousands | tens of thousands |