academic/CAFS_divergence: Added (functional shift clustering).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

1 files changed, 26 insertions, 0 deletions

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+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.