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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| .. | ||
| README | ec11283d0b academic/muscle: Update script and added manual page. | 4 years ago |
| References | 9b575230bb academic/muscle: Added (A multiple sequence alignments program) | 13 years ago |
| muscle.1 | ec11283d0b academic/muscle: Update script and added manual page. | 4 years ago |
| muscle.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 years ago |
| muscle.info | ec11283d0b academic/muscle: Update script and added manual page. | 4 years ago |
| slack-desc | ec11283d0b academic/muscle: Update script and added manual page. | 4 years ago |
README
MUSCLE is a program for creating multiple alignments of amino acid or
nucleotide sequences. A range of options is provided that give you the
choice of optimizing accuracy, speed, or some compromise between the
two.
Fast, accurate and easy to use
MUSCLE is one of the best-performing multiple alignment programs
according to published benchmark tests, with accuracy and speed that
are consistently better than CLUSTALW. MUSCLE can align hundreds of
sequences in seconds. Most users learn everything they need to know
about MUSCLE in a few minutes—only a handful of command-line options
are needed to perform common alignment tasks.
NOTE about the "-stable" option no longer being supported:
The "-stable" option had a bug, which sometimes resulted in incorrect
alignments to be produced. The author has created a python script to
be used as a workaround. The SlackBuild includes it and its usage is:
python muscle-stable.py input.fasta aligned.fasta > stable.fasta
Papers
There are two papers. The first (NAR) introduced the algorithm, and is
the primary citation if you use the program. The second (in BMC Bio-
informatics) gives more technical details, including descriptions of
non-default options.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity BMC Bioinformatics, (5) 113
nucleotide sequences. A range of options is provided that give you the
choice of optimizing accuracy, speed, or some compromise between the
two.
Fast, accurate and easy to use
MUSCLE is one of the best-performing multiple alignment programs
according to published benchmark tests, with accuracy and speed that
are consistently better than CLUSTALW. MUSCLE can align hundreds of
sequences in seconds. Most users learn everything they need to know
about MUSCLE in a few minutes—only a handful of command-line options
are needed to perform common alignment tasks.
NOTE about the "-stable" option no longer being supported:
The "-stable" option had a bug, which sometimes resulted in incorrect
alignments to be produced. The author has created a python script to
be used as a workaround. The SlackBuild includes it and its usage is:
python muscle-stable.py input.fasta aligned.fasta > stable.fasta
Papers
There are two papers. The first (NAR) introduced the algorithm, and is
the primary citation if you use the program. The second (in BMC Bio-
informatics) gives more technical details, including descriptions of
non-default options.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity BMC Bioinformatics, (5) 113