K9 is an Applescript Studio GUI front end for a variety of commonly performed functions in T-RFLP and community analysis.  While still in the advanced beta stages, K9 currently performs the following functions:

1.     Automatically cleans peak files generated by either GeneScan or Peak Scanner1.
   

2.     Filters and Bins peaks generated by either GeneScan or Peak Scanner1,2.
   

3.     Generates a Bray-Curtis distance matrix of peak data, performs a hierarchical clustering and    
   

        generates a dendrogram2,3.

1.     Rapidly builds one FASTA file from any number of individual sequence files.
   

2.     Provides a GUI interface to DOTUR4.
   

3.     Graph multiple chromatograms (individually and with 3D-overlay capacity)2,6.
   

4.     Generate a “Heat Map” of binned chromatogram data2,5.
   

5.     Graph rarefaction curves from DOTUR analyzed data (Shannon-weaver index is default)2
   

6.     Graphs Classification Data from the Ribosomal Database Project (RDP) as a function of                   
   

       database index.  This allows one to identify species present by clicking on the peaks.

    1 = based on slight modification so the perl script and R programs written by Zaid Abdo.   

    2 = requires R

    3 = requires the Vegan package for R

      4 = DOTUR, written by Patrick Schloss, is required for functionality.

    5 = requires the gplots package for R

    6 = requires the rgl package for R

    The computationally intensive nature of microbiome data analysis has resulted in a number of very clever methods of carrying out these analyses.  Unfortunately, most of these methods are not what one would call user-friendly.  Since, one of the purposes of the Microbiome Research Core was to facilitate cross disciplinary microbiome research, we decided to create an application which could take these tools and make them usable by anyone.  To that end we created K9.