Clusterfunc is a simple and fast method for Clustering functionally divergent genes by Functional Category.
Changes in protein structure and function are reflected at the level of amino acid sequence. This principle suggests that functional divergence - changes in protein function, for instance following gene duplication or new selective pressures - can be identified by analysis of primary sequence data. However, many amino acid substitutions have a negligible effect on protein function (see Kimura, 1983, "The neutral theory of molecular evolution"). This means that a simple comparison of the sequence differences between two clusters of homologous proteins will not reveal the subset of changes responsible for functional divergence.
Clusterfunc is one of several sequence-based methods for identifying that "interesting" subset of conserved, radical substitutions. The program can also cluster species based on similar profiles of functional divergence, revealing ecological adaptation. For more information on the scientific background for the method, see the user manual.
Clusterfunc is free, open-source software (GPL v3). We encourage you to download, use, and modify it for your own needs. If you have questions about installing or running the program, or the kind of scientific questions that can be answered with it, you could begin by reading the user manual and perhaps this paper, which uses an earlier version of the method:
Williams TA et al. (2010). Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet 26:47-51.
We have submitted a "methods" paper about Clusterfunc, and will update this page if/when it is published.
Alternatively, try posting a message on our discussion forum (see below).
Clusterfunc user manual:Clusterfunc
Mac snow leopard(10.6) intel binary:Clusterfunc
Mac leopard(10.5) intel binary:Clusterfunc
Windows binary(Needs Cygwin):Clusterfunc
Source Code:Clusterfunc source code
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