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diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README new file mode 100644 index 0000000000..b8b4a71a4b --- /dev/null +++ b/academic/vCAPS_coevolution/README @@ -0,0 +1,33 @@ +vCAPS: (verbose) Coevolution Analysis using Protein Sequences + +CAPS is aimed at measuring the coevolution between amino acid sites +belonging to the same protein (intra-molecular coevolution) or to two +functionally or physically interacting proteins (inter-molecular +coevolution). The Software implements an improved method to detect +intra-molecular coevolution as published in Genetics (Fares and Travers, +2006) and also inter-protein coevolution analysis. The improved scoring +of amino acid sites is obtained by maximum likelihood ancestral state +reconstruction along with simulations to assess significance. + +This is a modified version of "CAPS_coevolution", used in the AutoCoEv +pipeline: +https://github.com/mattilalab/autocoev + +It applies two _unofficial_ patches: +- 01_caps_verbose: makes the program output its generated trees, as well + as the p-value for each correlated amino acid pair +- 02_caps_sort_input: introduce a function to sort input file names + +The produced executable is called "vCAPS" and can be installed along +"caps" from CAPS_coevolution. Building CAPS from source requires the +Bio++ 1.9 suite libraries, but make sure the current versions of the +bppsuite (and its dependencies) are NOT installed at build time. + +Citing CAPS: +CAPS: coevolution analysis using protein sequences. Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a +further dimension to selective constraints analyses. Fares MA, Travers +SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113 |