slackbuilds/academic/aliview
Heinz Wiesinger 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var
Signed-off-by: Heinz Wiesinger <pprkut@slackbuilds.org>
2021-07-17 21:55:09 +02:00
..
README academic/aliview: Updated for version 1.23. 2018-06-17 22:44:42 +01:00
References academic/aliview: Updated for version 1.23. 2018-06-17 22:44:42 +01:00
aliview.SlackBuild All: Support $PRINT_PACKAGE_NAME env var 2021-07-17 21:55:09 +02:00
aliview.desktop academic/aliview: Added (Alignment viewer and editor). 2018-02-17 07:42:47 +07:00
aliview.info academic/aliview: update for version 1.27 + switch to adoptopenjdk 2021-05-18 23:40:05 +07:00
doinst.sh academic/aliview: Added (Alignment viewer and editor). 2018-02-17 07:42:47 +07:00
slack-desc academic/aliview: Added (Alignment viewer and editor). 2018-02-17 07:42:47 +07:00

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