Instructions for using FastGroupII with large data sets

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The FastGroup and FastGroupII programs were written by Forest Rohwer's group at San Diego State University. These programs were really written and tested on small 16S data sets typically from Sanger Sequencing. However, as is often the case, they work well for larger datasets like a single 454 run focussing on 16S genes.

FastGroup uses different clustering algorithms to generate both Richness (Chao1) and Diversity (Shannon-Wiener index) measures, as well as returning information about the groups and the statistics.


  • I recommend removing the trimming options (by unchecking the boxes) unless you have a specific sequence you want to trim to.
  • Please do not request the rarefaction curves These are computationally very expensive, and will take a long time to compute on large data sets.
  • For Mac users, the calculation may take some time to compute and return. I recommend using firefox rather than safari. The latter times out after a few minutes whereas firefox keeps waiting.
  • If you have problems with this site, please email the mg-rast mailing list. Although we do not control FastGroupII, we know the developers and will work with them. We are particularly concerned not to direct too much load on their server while we figure out a solution compatible with the mg-rast.