Tree:
331a473f1a
11.0
12.0
12.1
12.2
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
15.0-20230325.1
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14.2-20200424.1
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14.2-20200406.1
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14.2-20200328.1
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14.2-20200112.1
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14.2-20191231.1
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14.2-20191207.1
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14.2-20190427.1
14.2-20190420.1
14.2-20190413.1
14.2-20190406.1
14.2-20190330.1
14.2-20190323.1
14.2-20190316.1
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14.2-20190202.1
14.2-20190126.1
14.2-20190119.1
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14.2-20181229.1
14.2-20181225.1
14.2-20181222.1
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14.2-20181201.1
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14.2-20181117.1
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14.2-20181103.1
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14.2-20181020.1
14.2-20181013.1
14.2-20181006.1
14.2-20180929.1
14.2-20180923.1
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14.2-20180915.1
14.2-20180908.1
14.2-20180901.1
14.2-20180825.1
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14.2-20180811.1
14.2-20180804.1
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14.2-20180714.1
14.2-20180707.1
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14.2-20180609.1
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13.1-20100217.1
Heinz Wiesinger
63daf9f79a
All: Support $PRINT_PACKAGE_NAME env var
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3 years ago | |
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| .. | ||
| CAPS_coevolution.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 years ago |
| CAPS_coevolution.info | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 years ago |
| README | e14ced8086 academic/CAPS_coevolution: update Copyright years and README | 3 years ago |
| References | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 years ago |
| slack-desc | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 years ago |
README
CAPS: 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:
The script just repackages the binaries provided from upstream. If you
want to compile the program from source check "vCAPS_coevolution", which
also comes with an unofficial patch that extends the verbosity of the
results.
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
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:
The script just repackages the binaries provided from upstream. If you
want to compile the program from source check "vCAPS_coevolution", which
also comes with an unofficial patch that extends the verbosity of the
results.
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