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| author |   Petar Petrov <slackalaxy@gmail.com> | 2020-10-09 09:40:49 +0100 |
|---|---|---|
| committer |   Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2020-10-10 10:18:48 +0700 |
| commit | 2c2f50823f08c9c6cf9219e6a50dfdb1449d8769 (patch) | |
| tree | 5c5f2ba272216181c92ed78bba9dd028247feb3c /academic/vCAPS_coevolution/README | |
| parent | e4fea76d0129fd05e7138772f4714dca3994f853 (diff) | |
| download | slackbuilds-2c2f50823f08c9c6cf9219e6a50dfdb1449d8769.tar.gz slackbuilds-2c2f50823f08c9c6cf9219e6a50dfdb1449d8769.tar.xz | |
academic/vCAPS_coevolution: Added (Coevolution Analysis)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/vCAPS_coevolution/README')
| -rw-r--r-- | academic/vCAPS_coevolution/README | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README new file mode 100644 index 0000000000..51350cd21e --- /dev/null +++ b/academic/vCAPS_coevolution/README @@ -0,0 +1,29 @@ +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. + +In addition, a test which assesses whether two proteins are interacting +is implemented. + +NOTE: +This applies an _unofficial_ patch by Petrov et al 2020, to enable more +verbose output of the program, including CAPS generated phylogenetic +trees and p-values of the pairwise results. 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. + +CITING: +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 |