Overview of the process for analyzing microbial communities using FastGroupII. A) Protocol for high-throughput sequencing of environmental microbial communities. B) Protocol for 16S rDNA analyses used in FastGroupII. Sequences are trimmed and dereplicated according to user-specified parameters. FastGroupII can perform rarefaction analysis, and calculate the Chao1 richness estimator and the Shannon-Wiener diversity index. The output from FastGroupII is formatted for submission to sequence classification programs such as BLAST  and RDP Classifier .