Very little is known about prokaryotic diversity on coral reefs, the most biodiverse of all marine ecosystems. To address this issue we have been sequencing 16S rDNAs from Archaea and Bacteria associated with corals ^{(1, 2)}. To help with the analyses, the FastGroup project was started in 2001. FastGroup will take large 16S rDNA datasets, trim them, and determine community structure (e.g., dereplication).

The first version of FastGroup ⁽³⁾ was a Java program and can be downloaded here. FastGroupII is a web-based tool. It dereplicates large 16S rDNA libraries using several different algorithms, including the original FastGroup Percentage Sequence Identity (PSI), PSI with Gaps, Tree-parsing (ClustalW global alignment) ⁽⁴⁾, and Seq-Match (Sequence Match in Ribosomal Database Project) ⁽⁵⁾. FastGroupII also automatically calculates standard diversity and richness indexes, including the Shannon-Wiener index ⁽⁶⁾, Chao1 ⁽⁷⁾, and rarefaction ⁽⁸⁾.

Full online article: FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries, Yanan Yu, Mya Breitbart, Pat McNairnie and Forest Rohwer, BMC Bioinformatics 2006,7:57. Click here.

To use FastGroupII, click here.