Tree:
cc72a3d5d8
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
15.0-20230318.1
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15.0-20230107.1
15.0-20221231.1
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15.0-20221217.1
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14.2-20210417.1
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14.2-20200614.1
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14.2-20200424.1
14.2-20200419.1
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14.2-20200406.1
14.2-20200404.1
14.2-20200328.1
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14.2-20200112.1
14.2-20200103.1
14.2-20191231.1
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14.2-20190504.1
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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14.2-20190105.1
14.2-20181229.1
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14.2-20181222.1
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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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14.2-20180908.1
14.2-20180901.1
14.2-20180825.1
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14.2-20180804.1
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14.2-20180714.1
14.2-20180707.1
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14.2-20180609.1
14.2-20180602.1
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Heinz Wiesinger
63daf9f79a
All: Support $PRINT_PACKAGE_NAME env var
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3 years ago | |
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| .. | ||
| CAFS_divergence.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 years ago |
| CAFS_divergence.info | b56f1badba academic/CAFS_divergence: Added (functional shift clustering). | 7 years ago |
| README | b93bc3c89b academic/CAFS_divergence: Fix README. | 4 years ago |
| References | b56f1badba academic/CAFS_divergence: Added (functional shift clustering). | 7 years ago |
| slack-desc | b56f1badba academic/CAFS_divergence: Added (functional shift clustering). | 7 years ago |
README
CAFS: Clustering Analysis of Functional Shifts
CAFS is a simple and fast method for Clustering functionally divergent
(FD) genes by Functional Category.
The method implemented in CAFS is one of several sequence-based
methods for identifying the 'interesting' subset of substitutions
that might underpin functional divergence. These methods are based
on the idea of that functionally-important residues are highly
conserved, so that evolutionary rates tend to be low at important
sites. Functional divergence can then be identified by comparing
rates (or levels of conservation) between two clades of proteins at
a homologous site. Alternatively, a significant change in amino acid
identity (such as a large, positively-charged residue in one group of
sequences versus a small, neutral residue in the other) could indicate
functional divergence even without a change in rate.
This program analyses alignments and provides the user with the best
putative sites under functional divergence.
NOTE: This only repackages the 64bit binary provided from upstream. A
32bit executable is not available.
Citing:
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011).
Proteome-wide analysis of functional divergence in bacteria: Exploring a
host of ecological adaptations.
CAFS is a simple and fast method for Clustering functionally divergent
(FD) genes by Functional Category.
The method implemented in CAFS is one of several sequence-based
methods for identifying the 'interesting' subset of substitutions
that might underpin functional divergence. These methods are based
on the idea of that functionally-important residues are highly
conserved, so that evolutionary rates tend to be low at important
sites. Functional divergence can then be identified by comparing
rates (or levels of conservation) between two clades of proteins at
a homologous site. Alternatively, a significant change in amino acid
identity (such as a large, positively-charged residue in one group of
sequences versus a small, neutral residue in the other) could indicate
functional divergence even without a change in rate.
This program analyses alignments and provides the user with the best
putative sites under functional divergence.
NOTE: This only repackages the 64bit binary provided from upstream. A
32bit executable is not available.
Citing:
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011).
Proteome-wide analysis of functional divergence in bacteria: Exploring a
host of ecological adaptations.