Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

Contributors: Zaid Abdo, Ursel Schuette, Stephen Bent, Christopher Williams, Larry J. Forney, Paul Joyce

Contact: Zaid Abdo (zabdo@uidaho.edu)

Statistical analysis of T-RFLP data that include objective methods for:

1. determining a baseline so that “true” peaks in electropherograms can be identified,
2. a means to compare electropherograms and bin fragments of similar size,
3. clustering algorithms that can be used to identify communities that are similar to one another, and
4. a means to select samples that are representative of a cluster that can be used to construct 16S rRNA gene clone libraries.

About

• The programs are written in R, Perl and SAS.
• R is a language and environment for statistical computing and graphics. It is also free. (Download R and install.) Perl is also free. (Download Perl and install.)
• You will need to have access to the SAS. SAS is a commonly used commercial statistical software package. If you do not have SAS, you can learn more about purchasing this software by clicking here.
• Instructions to run these programs can be found here.
• The scripts can be downloaded from here.

• The paper can be downloaded here