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Andrew Clemons
351abefa6a
academic/aliview: Use zulu-openjdk11.
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2 년 전 | |
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| .. | ||
| README | a43d2d2e51 academic/aliview: Updated for version 1.23. | 6 년 전 |
| References | a43d2d2e51 academic/aliview: Updated for version 1.23. | 6 년 전 |
| aliview.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 2 년 전 |
| aliview.desktop | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 년 전 |
| aliview.info | 351abefa6a academic/aliview: Use zulu-openjdk11. | 2 년 전 |
| doinst.sh | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 년 전 |
| slack-desc | 19a57c0c92 academic/aliview: Added (Alignment viewer and editor). | 6 년 전 |
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
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