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14.2 > Academic > aliview (1.23)

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

This requires: jdk

Maintained by: Petar Petrov
Keywords: aliview,sequences,alignment,phylogeny,biology,bioinformatics,Petar Petrov
ChangeLog: aliview

Homepage:
http://www.ormbunkar.se/aliview/

Source Downloads:
aliview.tgz (b05a65ad2a70332343ef9ce6a28a9dcb)

Download SlackBuild:
aliview.tar.gz
aliview.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

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