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  Paul Joyce

University of Idaho


T-RFLP STATS

Statistical Methods for Characterizing Diversity of Microbial Communities by
Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA
Genes

 Statistical analysis of T-RFLP data that include objective methods for
(a) determining a baseline so that “true” peaks in electropherograms can be identified,
(b) a means to compare electropherograms and bin fragments of similar size,
(c) clustering algorithms that can be used to identify communities that are similar to one another, and
(d) a means to select samples that are representative of a cluster that can be used to
construct 16S rRNA gene clone libraries.


INSTRUCTIONS

  • 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.
  • Download, read and follow the instructions in the Manual (word file), before running these programs.
  • For Mac users download the following zipped directory.  Unzip and follow the instructions.

PROGRAMS
     
          Perl Script for Data entry into R   (AutomaticProgR.txt)

R Code    Filter and Binning       (FilteringandBinning.txt)
                Cover Program          (CoverProgram.txt)


SAS Macro                             (ClusteringMacroSingleuse.sas)


EXAMPLE DATA



If you have any questions on running these programs contact

Zaid Abdo                  zabdo@uidaho.edu