slackbuilds/academic/CAFS_divergence/README

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.