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Diffstat (limited to 'academic/vCAPS_coevolution/README')
| -rw-r--r-- | academic/vCAPS_coevolution/README | 22 |
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diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README index 51350cd21e..b8b4a71a4b 100644 --- a/academic/vCAPS_coevolution/README +++ b/academic/vCAPS_coevolution/README @@ -9,17 +9,21 @@ intra-molecular coevolution as published in Genetics (Fares and Travers, 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. +This is a modified version of "CAPS_coevolution", used in the AutoCoEv +pipeline: +https://github.com/mattilalab/autocoev -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. +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 -CITING: +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 |