Дерево:
331a473f1a
11.0
12.0
12.1
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13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
libressl-gopher-test
master
misc-fixes
python-renames
rworkman
urchlay
user/aclemons/updates
user/anddt/development/acpica
user/anddt/development/glm
user/anddt/development/gnustep-base
user/anddt/development/gnustep-make
user/anddt/games/assaultcube-reloaded
user/anddt/games/doomseeker
user/anddt/games/prboom-plus
user/anddt/games/rocksndiamonds
user/anddt/games/rottexpr
user/anddt/games/srb2
user/anddt/graphics/blender
user/anddt/graphics/maim
user/anddt/ham/chirp
user/anddt/ham/hamlib
user/anddt/libraries/girara
user/anddt/libraries/goffice
user/anddt/libraries/gtksourceview4
user/anddt/libraries/imlib2
user/anddt/libraries/jsoncpp
user/anddt/libraries/libnova
user/anddt/libraries/libopenmpt
user/anddt/libraries/libtorrent
user/anddt/libraries/wxGTK3
user/anddt/libraries/xmlrpc-c
user/anddt/misc/discount
user/anddt/misc/slop
user/anddt/network/nethogs
user/anddt/network/putty
user/anddt/network/rclone
user/anddt/network/rtorrent
user/anddt/network/sshguard
user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
user/anddt/system/zzzfm
user/belka/updates
user/chris.willing/updates
user/dslackw/updates
user/elyk/updates
user/kingbeowulf/updates
user/mario/updates
user/ponce/updates
user/pprkut/updates
willysr
wxWidgets-wip
GPG-KEY
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Petar Petrov
0a28023757
academic/vCAPS_coevolution: Added (Coevolution Analysis)
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2 лет назад | |
|---|---|---|
| .. | ||
| 01_caps_verbose.patch | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| 02_caps_sort_input.patch | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| README | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| References | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| slack-desc | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| vCAPS_coevolution.SlackBuild | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
| vCAPS_coevolution.info | 0a28023757 academic/vCAPS_coevolution: Added (Coevolution Analysis) | 2 лет назад |
README
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
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