CAFS: Clustering Analysis of Functional Shifts

CAFS is a simple and fast method for Clustering functionally divergent (FD)
genes by Functional Category.

The method implemented in CAFS is one of several sequence-based methods
for identifying the 'interesting' subset of substitutions that might
underpin functional divergence. These methods are based on the idea of that
functionally-important residues are highly conserved, so that evolutionary
rates tend to be low at important sites. Functional divergence can then be
identified by comparing rates (or levels of conservation) between two
clades of proteins at a homologous site. Alternatively, a significant
change in amino acid identity (such as a large, positively-charged residue
in one group of sequences versus a small, neutral residue in the other)
could indicate functional divergence even without a change in rate.

This program analyses alignments and provides the user with the best
putative sites under functional divergence.

NOTE: This only repackages the 64bit binary provided from upstream. A 32bit
executable is not available.

Citing:
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011).
Proteome-wide analysis of functional divergence in bacteria: Exploring a
host of ecological adaptations.
