slackbuilds_ponce/academic/aliview

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