Table 2 Speed of the 4 grouping methods in FastGroupII, and a comparison with FastGroup 1.0. The time in seconds was determined by trimming and grouping the 16S rDNA test dataset found on the FastGroupII website. A total of 621 sequences were dereplicated. A percentage sequence identity of 97% was used to group similar sequences in the PSI, PSI with Gaps and Tree-parsing method. A percentage sequence identity of 83% was used in the Seq-Match method.
From: FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Method | Time (s) |
|---|---|
PSI | 2 |
PSI with Gaps | 5 |
Seq-Match | 10 |
Tree-parsing | 7152 (ClustalW) + 0.1 (tree-parsing time) |
FastGroup 1.0 | 360 |