Table 1 |
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|
Comparison of WATERS' tools to existing web services and stand-alone software tools. |
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|
Greengenes |
RDP II |
RDP-Py |
Silva |
Mothur |
QIIME |
WATERS |
|
|
|
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|
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 |
|
|
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|
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. |
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|
Hartman et al. BMC Bioinformatics 2010 11:317 doi:10.1186/1471-2105-11-317 |
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