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diff --git a/academic/CAFS_divergence/README b/academic/CAFS_divergence/README new file mode 100644 index 0000000000..9320c24786 --- /dev/null +++ b/academic/CAFS_divergence/README @@ -0,0 +1,26 @@ +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. |