List of alignment visualization software

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This page is a subsection of the list of sequence alignment software.

Multiple alignment visualization tools typically serve four purposes:

  • Aid general understanding of large-scale DNA or protein alignments
  • Visualize alignments for figures and publication
  • Manually edit and curate automatically generated alignments
  • Analysis in depth

The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is necessary because algorithms for both multiple sequence alignment and structural alignment use heuristics which do not always perform perfectly. The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.

Alignment viewers, editors[edit]

Name Structure prediction tools integrated Can align sequences Can calculate phylogenetic trees Other features Format support License Link
Ale (emacs plugin) No Yes No No GenBank, EMBL, FASTA, PHYLIP Free, GPL Official website
AliView 2016 No MUSCLE integrated; other programs such as MAFFT can be defined External programs such as FastTree can be called from within Fast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design. FASTA, PHYLIP, Nexus, MSF, Clustal Free, GPL 3 Official website
Base-By-Base No MUSCLE UPGMA, NJ, complete and single linkages, WPMGA Visual summary, percent identity tables, some integrated advanced analysis tools Genbank, FASTA, EMBEL, Clustal, base-by-base files Proprietary, freeware, must register Official website
BioEdit No ClustalW Rudimentary, can read PHYLIP Plasmid drawing, ABI chromatograms, Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR Proprietary, freeware Official website
BioNumerics No Yes Yes ? Genbank, FASTA Proprietary, commercial Official website
BoxShade No No No Specifically for multiple alignments MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW Free, public domain Official website
CINEMA No, but can read-show 2D structure annotations ClustalW No Dotplot, 6 frame translation, Blast Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS Proprietary, freeware Official website
CLC viewer (free version) Commercial version only Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various UPGMA, NJ Workflows, blast-genbank search many Proprietary, freeware. More options available in commercial versions. Official website
ClustalX viewer No ClustalW NJ Alignment quality analysis Nexus, MSF, Clustal, FASTA, PHYLIP Proprietary, freeware for academic use Official website
Cylindrical Alignment App No No No 3D, animation, drilldown, legend selection BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT Free, CDDL 1. Available for dual licensing. Official website
Cylindrical BLAST Viewer No No No 3D, animation, drilldown, legend selection BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT Free, GPL Official website
DECIPHER Yes Yes UPGMA, NJ, ML Primer-Probe design, Chimera finding FASTA, FASTQ, GenBank Free, GPL Official website
Discovery Studio Yes Align123, ClustalW, S-ALIGN UPGMA, NJ, with bootstrap and best tree Visualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, more BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, ... Proprietary, commercial, Viewer is Freeware Official website
DnaSP ? ? ? Can compute several population genetics statistics, reconstruct haplotypes with PHASE FASTA, Nexus, MEGA, PHYLIP Proprietary, commercial, freeware for noncomercial use Official website
DNASTAR Lasergene Molecular Biology Suite Yes Yes Yes Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred Proprietary, commercial, academic licenses available Official website
emacs - biomode ? ? ? ? ? Free, GPL Official website
FLAK No Can perform fuzzy whole genome alignment No Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options FASTA Proprietary, commercial, freeware for noncommercial use Official website
Genedoc No, but can read-show annotations Pairwise No, but can read-show annotations gel simulation, stats, multiple views, simple many Proprietary, freeware Official website table of features
Geneious Yes - powered by EMBOSS tools Clustal, MUSCLE, MAUVE, profile, translation UPGMA, NJ, PhyML, MrBayes plugin, PAUP* plugin Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more >40 file formats imported and exported Proprietary, commercial; personal, floating Official website
Integrated Genome Browser (IGB) No No No Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers BAM, FASTA, PSL Free, CPL Official website
interactive Tree Of Life (iTOL) No No ? Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments. FASTA Proprietary, free use Official website
IVisTMSA No Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator ClustalW, MSF, PHYLIP, PIR, GDE, Nexus Proprietary, freeware Official website
Jalview 2 Secondary structure prediction via JNET Clustal, MUSCLE, MAFFT, Probcons, TCoffee via web services UPGMA, NJ Sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval. FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm Free, GPL Official website
Jevtrace Integrated with structure viewer WebMol No No A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. FASTA, MSF, Clustal, PHYLIP, Newick, PDB Proprietary, commercial, freeware for academic use Official website manual
JSAV No No No A JavaScript component allowing integrating an alignment viewer into web pages An array of JavaScript objects Free, GPL 2 Official website
Maestro Yes ClustalX Yes Mapping from sequence to 3D structure, structure-sequence editing-modeling Clustal, FASTA PDB Proprietary, freeware for academic use Official website
MEGA No Native ClustalW UPGMA, NJ, ME, MP, with bootstrap and confidence test Extended support to phylogenetics analysis FASTA, Clustal, Nexus, MEGA, etc. Proprietary, freeware, must register Official website No No No Optional coloring. Touching AA shows 3-letter code and sequence number. Touching consensus shows AA frequencies in that column. Counts and percentages of aromatics, charged, gaps. FASTA Free, Creative Commons Attribution NonCommercial Share-alike Official website
Multiseq (VMD plugin) No, but can display and align 3D structures ClustalW, MAFFT, Stamp (Structural) Percent identity, Clustal, MAFFT, Structural Scripting via Tcl, mapping from sequence to 3D structure FASTA, PDB, ALN, PHYLIP, NEXUS Proprietary, freeware, but VMD is free for noncommercial use only Official website
MView No No No Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF Free, GPL Official website
PFAAT No, but can display 3D structures ClustalW NJ Manual annotation, conservation scores Nexus, MSF, Clustal, FASTA, PFAAT Proprietary, freeware Official website
Ralee (emacs plugin for RNA al. editing) ? RNA structure ? ? Stockholm Free, GPL Official website
S2S RNA editor 2D structure Rnalign No Base-base interactions, 2D-3D viewer FASTA, RnaML Proprietary, freeware Official website
Seaview No local MUSCLE-ClustalW Parsimony, distance methods, PhyML Dot-plot, vim-like editing keys Nexus, MSF, Clustal, FASTA, PHYLIP, MASE Proprietary, freeware Official website
Seqotron No MUSCLE, MAFFT UPGMA, NJ, ML (Physher) Manual alignment, tree visualisation; runs on Mac OS X Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat Free, GPL Official website publication
Sequilab Yes Yes No Link alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbars Accession number, GI number, PDB ID, FASTA, drag-drop from external URL from within the user interface Proprietary, freeware Official website
SeqPop No ? ? ? ? Proprietary, freeware Official website
Sequlator No Pairwise alignment No easy alignment editing MSF Proprietary, freeware Official website
SnipViz No No No (but can display them) Pure Javascript and HTML; suitable to integrate in websites FASTA, newick Free, Apache 2.0 Official website, publication
Strap Jnet, NNPREDICT, Coiled coil, 16 different TM-helix 15 different methods NJ Dot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, BioJava-interface MSF, Stockholm, ClustalW, Nexus, FASTA, PDB, Embl, GenBank, hssp, Pfam Free, GPL Official website
Tablet No No No High-performance graphical viewer for viewing next generation sequence assemblies and alignments. ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3 Free, BSD 2-clause Official website
UGENE Yes MUSCLE, Kalign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith–Waterman algorithm Yes Many FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFF Free, GPL Official website
VISSA sequence-structure viewer DSSP secondary structure ClustalX No Mapping from sequence to 3D structure Clustal, FASTA Proprietary, freeware Official website
DNApy No MUSCLE No Editing of GenBank files, plasmid drawing, ABI chromatograms, FASTA, FASTQ, GenBank Free, GPL 3 Official website
Alignment Annotator Yes By sequence or mixed sequence and structure Includes Archaeopteryx Running in modern web browsers of desktop PCs, tablets (iOS, Android, MS-Mobile). DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview. Many Free, GPL Official website

Some useful discussions on sequence alignment editors/viewers can be found here:

See also[edit]