| |
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.
