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U.S. Geological Survey - Great Lakes Science Center

Cluster Analysis Program (BOOTCLUS)

A program designed to read a standard species abundance data file and produce an agglomerative, hierarchical cluster analysis and bootstrap each linkage to test for significance. BOOTCLUS version 3.1 now includes much better file access capabilities. The same ASCII text input and output files are used, but the Windows general dialogue box for locating files is now available. Simply click on the box for the file pathname (input or output) and the dialog box will appear. It functions like that in other Windows applications. The other new feature is an output list with letters (or symbols) identifying cluster membership for each sample of the input dataset. This list is printed at the end of the output file and includes only the sample label and a letter associating that sample with a given cluster identified by the analysis. This output list can be easily inserted into a spreadsheet with the original input data and used to sort the samples according to cluster membership. Letters identifying each cluster are assigned in the order in which fusions occur (not left to right across the dendrogram). The first 52 clusters are identified by letters (A - AZ). Subsequent clusters are identified by a combination of a letter and an ASCII symbol (e.g., [, ], ^, etc.). This version of BOOTCLUS uses the same algorithm and coding for analysis, but the new features have not been tested as extensively as the core of the program. Please treat this relase as a beta version and always double check the cluster designations provided in the final list against the dendrogram and the significance test.

Downloads & Instructions

Download the file containing each of the three setup files (SETUP.EXE, SETUP.LST, and BOOTCLUS.CAB) to a work area on your computer's hard drive. Then unzip the file, run the setup.exe program and follow the instructions. The BOOTCLUS program can then be run from the Programs selection menu of the Start menu.

Some people have had trouble installing this program, particularly if they have another version already installed. If you receive an error message about updating Windows files and that update simply will not occur to the satisfaction of the install program, then download the, unzip the file, and copy the BOOTCLUS.EXE file to your hard drive, over-writing the old one. The program should then run successfully and there will be no need to go through the install process.


The example uses weighted fish count data from several coral reef areas in the Dry Tortugas (see McKenna J.E. 1997. Influence of physical disturbance on the structure of coral reef fish assemblages in the Dry Tortugas. Caribbean Journal of Science 33:82-97. for details). Download and unzip the file to your computer's hard drive. The FISHBIO.MTX is the input file. FISHBIO.AVG contains a file structured like the input file, but samples are averages of replicates from the original input file. Output is found in FISHBIO.cls.

Send questions and comments on this program to Dr. Jim McKenna, Tunision Laboratory of Aquatic Science,

McKenna, J. E. Jr. 2003. An enhanced cluster analysis program with bootstrap significance testing for ecological community analysis. Environmental Modelling & Software 18(3): 205-220.

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