目錄樹:
cc72a3d5d8
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
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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
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user/anddt/libraries/xmlrpc-c
user/anddt/misc/discount
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user/anddt/network/putty
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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
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user/ponce/updates
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willysr
wxWidgets-wip
GPG-KEY
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Andrew Clemons
351abefa6a
academic/aliview: Use zulu-openjdk11.
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2 年之前 | |
|---|---|---|
| .. | ||
| README | a43d2d2e51 academic/aliview: Updated for version 1.23. | 6 年之前 |
| References | a43d2d2e51 academic/aliview: Updated for version 1.23. | 6 年之前 |
| aliview.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 年之前 |
| aliview.desktop | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 年之前 |
| aliview.info | 351abefa6a academic/aliview: Use zulu-openjdk11. | 2 年之前 |
| doinst.sh | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 年之前 |
| slack-desc | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 年之前 |
README
AliView is yet another alignment viewer and editor, but this is
probably one of the fastest and most intuitive to use. Features:
- fast and light-weight
- simple navigation, mouse-wheel zoom out and zoom in
- highlight consensus characters or characters deviating
- edit sequences/alignment (manually)
- align, add and align automatically with any aligner of your choice
- align new sequences to existing or realign all
- realign a selected block
- realign nucleotides as translated amino-acids
- delete vertical gaps
- undo/redo
- find degenerate primers in conserved regions in an alignment
- open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format
- print (current view)
- export whole alignment as an image file (png-format)
- copy selection (as fasta-sequences or just characters)
- paste sequences (as sequences or filenames)
- add more sequences from file
- merge two sequences - and calculate consensus
- translate (view) nucleotide sequences as amino-acid sequences
- save translated alignment
- read / preserve Codonpos, Charset and Excludes (Nexus-specification)
- change Codonpos for selected regions (Nexus-specification)
- drag-drop/remove of sequences/files
- move sequences to top/bottom with key-stroke
- a simple "external interface" that lets you invoke other programs
- search function that finds patterns across gaps and follows IUPAC
- search multiple sequence names at once (stored in clipboard)
- reverse complement/reverse/complement sequences or whole alignment
- different color schemes
- sort sequences by name
- sort sequences by residue in selected column
Citation:
Larsson, A. (2014). AliView: a fast and lightweight alignment viewer
and editor for large data sets. Bioinformatics30(22): 3276-3278.
http://dx.doi.org/10.1093/bioinformatics/btu531
probably one of the fastest and most intuitive to use. Features:
- fast and light-weight
- simple navigation, mouse-wheel zoom out and zoom in
- highlight consensus characters or characters deviating
- edit sequences/alignment (manually)
- align, add and align automatically with any aligner of your choice
- align new sequences to existing or realign all
- realign a selected block
- realign nucleotides as translated amino-acids
- delete vertical gaps
- undo/redo
- find degenerate primers in conserved regions in an alignment
- open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format
- print (current view)
- export whole alignment as an image file (png-format)
- copy selection (as fasta-sequences or just characters)
- paste sequences (as sequences or filenames)
- add more sequences from file
- merge two sequences - and calculate consensus
- translate (view) nucleotide sequences as amino-acid sequences
- save translated alignment
- read / preserve Codonpos, Charset and Excludes (Nexus-specification)
- change Codonpos for selected regions (Nexus-specification)
- drag-drop/remove of sequences/files
- move sequences to top/bottom with key-stroke
- a simple "external interface" that lets you invoke other programs
- search function that finds patterns across gaps and follows IUPAC
- search multiple sequence names at once (stored in clipboard)
- reverse complement/reverse/complement sequences or whole alignment
- different color schemes
- sort sequences by name
- sort sequences by residue in selected column
Citation:
Larsson, A. (2014). AliView: a fast and lightweight alignment viewer
and editor for large data sets. Bioinformatics30(22): 3276-3278.
http://dx.doi.org/10.1093/bioinformatics/btu531