Nucleotides realigned as translated AminoAcids and then retranslated to nucleotidesĭelete sequences, reorder, move to top, move to bottom Realign single sequence with MUSCLE or other aligner program Realign selected block with muscle or other aligner program MUSCLE or other alignment program to realign sequences Highlight characters belonging to Consensus Highlight characters deviating from selected "Trace" sequence Highlight characters deviating from Consensus View nucleotides colored as translated Amino Acids (1-position) View nucleotides colored as translated Amino Acids Reads unlimited size FASTA, PHYLIP, NEXUS, CLUSTAL and MSF files Unlimited mouse wheel zoom in/out to see whole alignment sort sequences by residue in selected column different color schemes including ClustalX reverse complement/reverse/complement sequences or whole alignment search multiple sequence names at once (stored in clipboard)
search function that finds patterns across gaps and follows IUPAC codes To FastTree and then automatically opened in FigTree) a very simple to use "external interface" that lets you invoke your other favorite programs (you could for example automatically have the alignment sent move sequences to top/bottom with key-stroke change Codonpos for selected regions (Nexus-specification) read and preserve Codonpos, Charset and Excludes (Nexus-specification) translate (view) nucleotide sequences as amino-acid sequences
merge two sequences - and calculate consensus if the overlap is not perfect paste sequences (both as sequences in clipboard or filenames in clipboard) copy selection (as fasta-sequences or just characters) export whole alignment as an image file (png-format) open and save in FASTA-, NEXUS-, PHYLIP, CLUSTAL or MSF-format (unlimited file sizes) find degenerate primers in conserved regions in an alignment of mixed species realign nucleotides as translated amino-acids align new sequences to existing or realign all define aligner program presets (different parameters, different software) align, add and align automatically with MUSCLE (included) or MAFFT, or any edit sequences/alignment (manually), insert, delete, change, move, rename various visual cues to highlight consensus characters or characters deviatingįrom the consensus or characters deviating from a selected "trace"-sequence simple navigation, mouse-wheel zoom out unlimited to see whole alignment, and
#.exe viewer for mac software license#
The program is released under the Open Source Software License 'GNU General Public License, version 3.0 (GPLv3)'ĭownload the latest stable version: 1.27 (09/Mar/2021) (Mac OS X, Windows, Linux) AliView: a fast and lightweight alignment viewer and editor for large data sets. University, so there is probably a predominance in functionality supportingĬitation: Larsson, A. The program is developed at the department of Systematic Biology, Uppsala It is of course also working very well with smaller datasets:) Transcriptome datasets initiated the design of the program. The speed in rendering even makes it possible to work with large alignments on older hardware.Ī need to easily sort, view, remove, edit and merge sequences from large The general idea when designing this program has always been usability and speed, all new functions are optimized so they do not affect the general performance and capability to work swiftly with large alignments. Of the fastest and most intuitive to use, not so bloated and hopefully to your AliView is yet another alignment viewer and editor, but this is probably one
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