From b93bc3c89b295981b9131a6aced3c0948c328e6b Mon Sep 17 00:00:00 2001 From: B. Watson Date: Thu, 8 Oct 2020 16:46:13 -0400 Subject: academic/CAFS_divergence: Fix README. Signed-off-by: B. Watson Signed-off-by: Willy Sudiarto Raharjo --- academic/CAFS_divergence/README | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) (limited to 'academic') diff --git a/academic/CAFS_divergence/README b/academic/CAFS_divergence/README index 9320c24786..61ae3acb06 100644 --- a/academic/CAFS_divergence/README +++ b/academic/CAFS_divergence/README @@ -1,24 +1,25 @@ CAFS: Clustering Analysis of Functional Shifts -CAFS is a simple and fast method for Clustering functionally divergent (FD) -genes by Functional Category. +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. +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. +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). -- cgit v1.2.3