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diff --git a/academic/aliview/README b/academic/aliview/README new file mode 100644 index 0000000000000..d9e65dc923e6a --- /dev/null +++ b/academic/aliview/README @@ -0,0 +1,39 @@ +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 |