K-Shuff

K-shuff is a powerful computer program designed to identify spatial clustering in a given dataset based on the reduced second moment measure, or K-function. In essence, K-shuff can be adapted for comparing any data from two (or more) samples to understand their relationship with each other. As an example, we adapt this technique to compare 16S rRNA gene sequence libraries from different environmental samples by treating gene sequences as points in space with hundreds of dimensions.


Download K-shuff. Click here to download the latest beta version of K-shuff for testing.

NOTE: The current version of K-shuff was successfully tested with an input distance matrix of upto 4000 sequences on a Windows-PC with 2.8 GHz processor and 4 GB RAM. Under these conditions, the analysis was completed in less than 25 minutes including random permutations. Run times increase slightly if you have more comparisons, i.e., number of libraries within the same distance matrix size.


Download WSCF-dataset. Click here to download the WSCF-dataset used in K-shuff.


Download K-shuff User Manual: Click here to download the K-shuff user manual. If you wish to use K-shuff for your research, please contact Prof. William Whitman.