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40 lines
1.8 KiB
Text
40 lines
1.8 KiB
Text
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AliView is yet another alignment viewer and editor, but this is
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probably one of the fastest and most intuitive to use. Features:
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- fast and light-weight
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- simple navigation, mouse-wheel zoom out and zoom in
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- highlight consensus characters or characters deviating
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- edit sequences/alignment (manually)
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- align, add and align automatically with any aligner of your choice
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- align new sequences to existing or realign all
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- realign a selected block
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- realign nucleotides as translated amino-acids
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- delete vertical gaps
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- undo/redo
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- find degenerate primers in conserved regions in an alignment
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- open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format
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- print (current view)
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- export whole alignment as an image file (png-format)
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- copy selection (as fasta-sequences or just characters)
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- paste sequences (as sequences or filenames)
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- add more sequences from file
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- merge two sequences - and calculate consensus
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- translate (view) nucleotide sequences as amino-acid sequences
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- save translated alignment
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- read / preserve Codonpos, Charset and Excludes (Nexus-specification)
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- change Codonpos for selected regions (Nexus-specification)
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- drag-drop/remove of sequences/files
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- move sequences to top/bottom with key-stroke
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- a simple "external interface" that lets you invoke other programs
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- search function that finds patterns across gaps and follows IUPAC
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- search multiple sequence names at once (stored in clipboard)
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- reverse complement/reverse/complement sequences or whole alignment
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- different color schemes
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- sort sequences by name
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- sort sequences by residue in selected column
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Citation:
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Larsson, A. (2014). AliView: a fast and lightweight alignment viewer
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and editor for large data sets. Bioinformatics30(22): 3276-3278.
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http://dx.doi.org/10.1093/bioinformatics/btu531
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