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.

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

Yu et al. BMC Bioinformatics 2006 7:57   doi:10.1186/1471-2105-7-57