View source for List of alignment visualization software

{{Short description|none}}
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 ==
{| class="wikitable sortable"
|-
! Name
! Structure prediction tools integrated
! Can align sequences
! Can calculate phylogenetic trees
! Other features
! Format support
! [[Software license|License]]
!Can run on Browser
!Operating Platforms
! Link
|-
| Alan
| {{no}}
| {{no}}
| {{no}}
| Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding
| [[FASTA format|FASTA]], [[Clustal]]
| {{free}}, [[GNU General Public License|GPL]] 3
|No
|Linux Terminal
| {{Official website|https://github.com/mpdunne/alan}}
|-
| Ale ([[emacs]] plugin)
| {{no}}
| {{yes}}
| {{no}}
| {{no}}
| GenBank, EMBL, [[FASTA format|FASTA]], [[PHYLIP]]
| {{free}}, [[GNU General Public License|GPL]]
|No
|GNU Emacs
| {{Official website|www.red-bean.com/ale}}
|-
| AliView 2025
| {{no}}
| {{yes|MUSCLE integrated; other programs such as MAFFT can be defined}}
| {{some|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 format|FASTA]], [[FASTQ]], [[PHYLIP]], [[Nexus file|Nexus]], MSF, [[Clustal]]
| {{free}}, [[GNU General Public License|GPL]] 3
|?
|Cross-platform -Mac OS, 

Linux, 

Windows
| {{Official website|www.ormbunkar.se/aliview}}
|-
| alv
| {{no}}
| {{no}}
| {{no}}
| Console-based (no GUI), yet with colors. Coding DNA is coloured by codon.
| [[FASTA format|FASTA]], [[PHYLIP]], [[Nexus file|Nexus]], [[Clustal]], [[Stockholm format|Stockholm]]
| {{free}}, [[GNU General Public License|GPL]] 3
| No
|Cross-platform
| {{Official website|https://pypi.org/project/alv/}}, see also {{GitHub|https://github.com/arvestad/alv}}
|-
| [[ARB_Project|arb]]
| {{yes|structure editable, show bond in helix sequence regions, 2D molecule viewer}}
| {{yes|MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)}}
| {{yes|arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayes}}
| Edits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and [http://www.arb-home.de/images/arb_secedit_large.png visualizes probes].
| [[FASTA format|FASTA]], [[GenBank]], [[EMBL]], [[Newick format|Newick]]
| {{proprietary}}, [[freeware]], [http://vc.arb-home.de/readonly/trunk/arb_LICENSE.txt arb license], open modifiable source
| No
|Linux, Mac OS (homebrew)
| {{Official website|http://www.arb-home.de/}}
|-
| Base-By-Base
| {{no}}
| {{yes|MUSCLE}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], complete and single linkages, WPMGA}}
| Visual summary, percent identity tables, some integrated advanced analysis tools
| Genbank, [[FASTA format|FASTA]], EMBEL, [[Clustal]], base-by-base files
| {{proprietary}}, [[freeware]], must register
|?
|?
| {{Official website|athena.bioc.uvic.ca/virology-ca-tools/base-by-base}}
|-
| BioEdit
| {{no}}
| {{yes|[[Clustal]]W}}
| {{some|Rudimentary, can read [[PHYLIP]]}}
| Plasmid drawing, ABI chromatograms,
| Genbank, [[FASTA format|FASTA]], [[PHYLIP]] 3.2 and 4, NBRF-PIR
| {{proprietary}}, [[freeware]]
|No
|Windows (95/98/NT/2000/XP)
| {{Official website|www.mbio.ncsu.edu/BioEdit/bioedit.html}}
|-
| [[BioNumerics]]
| {{no}}
| {{yes}}
| {{yes}}
| {{dunno}}
| Genbank, [[FASTA format|FASTA]]
| {{proprietary}}, [[Commercial software|commercial]]
|?
|?
| {{Official website|www.applied-maths.com/bionumerics/bionumerics.htm}}
|-
| bioSyntax
| {{no}}
| {{no}}
| {{no}}
| Native syntax highlighting support for [[Vim_(text_editor)|Vim]], [[Less_(Unix)|less]], [[gedit]] and [[Sublime_Text|Sublime]]
| [[FASTA]], [[FASTQ]], [[Clustal]], [[SAM_(file_format)|SAM]], [[Variant_Call_Format|VCF]] and more
| {{free}}, [[GNU General Public License|GPL]] 3
|No
|Vim, Less, GEdit, & Sublime
| {{Official website|https://bioSyntax.org}}
|-
| BoxShade
| {{no}}
| {{no}}
| {{no}}
| Specifically for multiple alignments
| MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by [[Clustal]]W
| {{free}}, [[public domain]]
|No
|MSDOS, VMS
| {{Official website|ch.embnet.org/software/BOX_form.html}}
|-
| CINEMA
| {{no}}, but can read-show 2D structure annotations
| {{yes|[[Clustal]]W}}
| {{no}}
| Dotplot, 6 frame translation, Blast
| [[Nexus file|Nexus]], MSF, [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP]], [[Protein Information Resource|PIR]], PRINTS
| {{proprietary}}, [[freeware]]
|No
|Cross-platform -Mac OS, Linux, Windows 
| {{Official website|aig.cs.man.ac.uk/research/utopia/cinema/cinema.php}}
|-
| CLC viewer (free version)
| {{some|Commercial version only}}
| {{yes|[[Clustal]], MUSCLE, T-Coffee, MAFFT, Kalign, various}}
| {{yes|UPGMA, [[Neighbor joining|NJ]]}}
| Workflows, blast-genbank search
| many
| {{proprietary}}, [[freeware]]. More options available in commercial versions.
|No
|?
| {{Official website|www.clcbio.com}}
|-
| CIAlign
| {{no}}
| {{no}}
| {{no}}
| Alignment visualisation as publication-ready images, alignment cleaning.
| [[FASTA format|FASTA]]
| {{free}}, [[MIT License|MIT]]
| No
| Linux, Windows, MacOS
| {{Official website|https://github.com/KatyBrown/CIAlign}} 
[[doi:10.7717/peerj.12983|Publication]]
|-
| [[Clustal]]X viewer
| {{no}}
| {{yes|[[Clustal]]W}}
| {{yes|[[Neighbor joining|NJ]]}}
| Alignment quality analysis
| [[Nexus file|Nexus]], MSF, [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP]]
| {{proprietary}}, [[freeware]] for academic use
|No
|Command line
| {{Official website|www.clustal.org}}
|-
| [[CodonCode Aligner]]
| {{no | no, but can read, add & show structure annotations}}
| {{yes|[[Clustal]], MUSCLE, various built-in algorithms}}
| {{yes| Yes}}
| Multi- and pairwise alignments, assembly, sequence translation, editing, trimming, mutation detection, restriction analysis, cloning, primer design, dotplot, much more
| ABI, SCF, [[FASTA format|FASTA]], FASTQ, [[Nexus file|Nexus]]/PAUP or [[PHYLIP]], Sam, Bam, .dna, EMBL, GenBank, BLAST, GFF
| {{proprietary}}, [[Commercial software|commercial]], Viewer is [[Freeware]]
|No
|Mac OS, Windows
| {{Official website|www.codoncode.com/aligner}}
|-
| Cylindrical Alignment App
| {{no}}
| {{no}}
| {{no}}
| 3D, animation, drilldown, legend selection
| BLAST XML, proprietary XML, GFF3, [[Clustal]]W, INSDSet, user expandable with [[XSLT]]
| {{free}}, [[Common Development and Distribution License|CDDL 1.]] Available for dual licensing.
|?
|Cross-platform -Mac OS, Linux, Windows
| {{Official website|sourceforge.net/projects/cylindrical-alignment-app}}
|-
| Cylindrical BLAST Viewer
| {{no}}
| {{no}}
| {{no}}
| 3D, animation, drilldown, legend selection
| BLAST XML, proprietary XML, GFF3, [[Clustal]]W, INSDSet, user expandable with [[XSLT]]
| {{free}}, [[GNU General Public License|GPL]]
|?
|?
| {{Official website|sourceforge.net/projects/cyl-viewer}}
|-
| DECIPHER
| {{yes}}
| {{yes}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], ML}}
| Primer-Probe design, Chimera finding
| FASTA, FASTQ, GenBank
| {{free}}, [[GNU General Public License|GPL]]
|No
|Mac OS, Windows
| {{Official website|decipher.cee.wisc.edu/Download.html}}
|-
| Discovery Studio
| {{yes}}
| {{yes|Align123, [[Clustal]]W, S-ALIGN}}
| {{yes|UPGMA, [[Neighbor joining|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, [[Protein Data Bank (file format)|PDB]], SEQ, SPT, ...
| {{proprietary}}, [[Commercial software|commercial]], Viewer is [[Freeware]]
|?
|Linux, Windows
| {{Official website|accelrys.com/products/discovery-studio/visualization-download.php}}
|-
| DnaSP
| {{dunno}}
| {{dunno}}
| {{dunno}}
| Can compute several population genetics statistics, reconstruct haplotypes with PHASE
| [[FASTA]], [[Nexus file|Nexus]], MEGA, [[PHYLIP]]
| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for noncommercial use
|?
|Cross-platform -Mac OS, Linux, Windows
| {{Official website|www.ub.es/dnasp}}
|-
| [[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 format|FASTA]], GCG Pileup, GenBank, Phred
| {{proprietary}}, [[Commercial software|commercial]], academic licenses available
|?
|Mac OS, Windows
| {{Official website|www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx}}
|-
| [[emacs]] - biomode
| {{dunno}}
| {{dunno}}
| {{dunno}}
| {{dunno}}
| {{dunno}}
| {{free}}, [[GNU General Public License|GPL]]
|?
|?
| {{Official website|archive.debian.net/lenny/biomode}}
|-
| FLAK
| {{no}}
| {{some|Can perform fuzzy whole genome alignment}}
| {{no}}
| Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options
| FASTA
| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for noncommercial use
|?
|?
| {{Official website|flakbio.com}}
|-
| Genedoc
| {{no}}, but can read-show annotations
| {{some|Pairwise}}
| {{no}}, but can read-show annotations
| gel simulation, stats, multiple views, simple
| many
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|www.nrbsc.org/gfx/genedoc}} [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features]
|-
| Geneious
| {{yes}} - powered by [[EMBOSS]] tools
| {{yes|[[Clustal]], MUSCLE, MAUVE, profile, translation}}
| {{yes|UPGMA, [[Neighbor joining|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 software|commercial]]; personal, floating
|?
|Cross-platform - Mac, Windows, Linux
| {{Official website|www.geneious.com}}
|-
| [[Integrated Genome Browser]] (IGB)
| {{no}}
| {{no}}
| {{no}}
| Sequences and features from files, URLs, and arbitrary [[Distributed Annotation System|DAS]] and QuickLoad servers
| BAM, [[FASTA format|FASTA]], PSL
| {{free}}, [[Common Public License|CPL]]
|?
|Cross-platform - Mac, Windows, Linux
| {{Official website|igb.bioviz.org}}
|-
| interactive Tree Of Life (iTOL)
| {{no}}
| {{no}}
| {{dunno}}
| 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
|Yes
|Browser
| {{Official website|itol.embl.de}}
|-
| IVisTMSA
| {{no}}
| {{yes|[[Clustal]] Omega, ClustalW2, MAFFT, MUSCLE, [[BioJava]] are integrated to construct alignment}}
| {{yes|Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using [[Archaeopteryx (evolutionary tree visualization and analysis)|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 format|FASTA]] generator and MSA ID matrix calculator  
| [[Clustal]]W, MSF, [[PHYLIP]], [[Protein Information Resource|PIR]], GDE, Nexus 
| {{proprietary}}, [[freeware]]
|?
|?
| www.ivistmsa.com
|-
| [[Jalview]]
| {{yes|Secondary structure prediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JPred 4]}}
| {{yes|[[Clustal#Clustal_Omega|Clustal O]], [[Clustal]], GLprobs, MSAprobs, [[MUSCLE (alignment software)|MUSCLE]], [[MAFFT]], Probcons, TCoffee, via web services}}
| {{yes|[[UPGMA]], [[Neighbor joining|NJ]]}}
| Sequences and features retrieved from user-configurable and publicly registered servers, e.g. [[European_Molecular_Biology_Laboratory|EMBL]], [[European_Bioinformatics_Institute|EBI]], [[Protein_Data_Bank|PDB]], [[Pfam]], [[Rfam]], [[UniProt]] Accession retrieval.  Structure/model data retrieval from [[Protein_Data_Bank|PDB]] and 3D-Beacons including [[Protein_Data_Bank|PDBe]], [[AlphaFold#Protein_Structure_Database|AlphaFold DB]], [[Swiss-model|SWISS-MODEL]].
| [[FASTA format|FASTA]], [[Pfam]], MSF, [[Clustal]], BLC, [[Protein Information Resource|PIR]], [[Stockholm format|Stockholm]], [[Variant_Call_Format|VCF]], AMSA, BioJSON, Clustal, [[European_Nucleotide_Archive#EMBL-Bank_format|ENA]], [[GenBank]], [[General_feature_format|GFF2]], [[General_feature_format|GFF3]], JnetFile, [[PHYLIP]], [[Pileup_format|PileUp]], RNAML, [[Crystallographic_Information_File|CIF]], [[Crystallographic_Information_File|mmCIF]], [[Protein_Data_Bank_(file_format)|PDB]].
| {{free}}, [[GNU General Public License|GPL]]
|[https://www.jalview.org/jalview-js/ JalviewJS] (Javascript)
|Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine.
| {{Official website|https://www.jalview.org/}}
|-
| Jevtrace
| {{some|Integrated with structure viewer [http://www.cmpharm.ucsf.edu/~walther/webmol.html WebMol]}}
| {{no}}
| {{no}}
| A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive [https://www.ncbi.nlm.nih.gov/pubmed/8609628 Evolutionary Trace] and other phylogeny inspired analysis.
| [[FASTA format|FASTA]], MSF, [[Clustal]], [[PHYLIP]], [[Newick format|Newick]], [[Protein Data Bank (file format)|PDB]]
| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for academic use
|?
|Cross-platform -Mac OS,  Linux, 

Windows
| {{Official website|compbio.berkeley.edu/people/marcin/jevtrace}} [http://compbio.berkeley.edu/people/marcin/jevtrace/jevtracev3.12_manual.pdf manual]
|-
| JSAV
| {{no}}
| {{no}}
| {{no}}
| A JavaScript component allowing integrating an alignment viewer into web pages
| An array of JavaScript objects
| {{free}}, [[GNU General Public License|GPL]] 2
|Yes
|Browser
| {{Official website|www.bioinf.org.uk/software/jsav}}
|-
|Lucid Align| Lucid Align
| {{no}}
| {{no}}
| {{no}}
|BAM, FASTQ, FASTA| Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data 
|BAM, FASTQ, FASTA
| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for academic use
|No
|Mac OS
|{{Official website|https://www.lucidalign.com}}
|-
| Maestro
| {{yes}}
| {{yes|[[Clustal]]X}}
| {{yes}}
| Mapping from sequence to 3D structure, structure-sequence editing-modeling
| [[Clustal]], [[FASTA format|FASTA]] [[Protein Data Bank|PDB]]
| {{proprietary}}, [[freeware]] for academic use
|?
|?
| {{Official website|www.schrodinger.com/products/14/12}}
|-
| [[MEGA, Molecular Evolutionary Genetics Analysis|MEGA]]
| {{no}}
| {{yes|Native [[Clustal]]W}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], ME, MP, with bootstrap and confidence test}}
| Extended support to phylogenetics analysis
| FASTA, [[Clustal]], Nexus, MEGA, etc.
| {{proprietary}}, [[freeware]], must register
|?
|?
| {{Official website|www.megasoftware.net}}
|-
| [[Molecular Operating Environment]] (MOE)
| {{yes}}
| {{yes}}
| {{yes}}
| Part of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc.
| [[Clustal]], [[FASTA format|FASTA]], [[Protein Data Bank|PDB]], EMBL, GCG, GCG_MSF, Genbank, [[PHYLIP]], [[Protein Information Resource|PIR]], raw_seq
| {{proprietary}}
|?
|?
| {{Official website|www.chemcomp.com/MOE-Molecular_Operating_Environment.htm}}
|-
| MSAReveal.org
| {{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 license|Creative Commons]] Attribution NonCommercial [[Share-alike]]
|?
|?
| {{Official website|msareveal.org}}
|-
| Multiseq ([[Visual Molecular Dynamics|VMD]] plugin)
| {{no}}, but can display and align 3D structures
| {{yes|[[Clustal]]W, MAFFT, Stamp (Structural)}}
| {{yes|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|www.scs.illinois.edu/schulten/multiseq}}
|-
| MView
| {{no}}
| {{no}}
| {{no}}
| Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns
| BLAST search, [[FASTA format|FASTA]] search, [[Clustal]], HSSP, [[FASTA format|FASTA]], [[Protein Information Resource|PIR]], MSF
| {{free}}, [[GNU General Public License|GPL]]
|No
|Cross-platform - Mac OS, Linux, Windows
| {{Official website|desmid.github.io/mview}}
|-
| PFAAT
| {{no}}, but can display 3D structures
| {{yes|[[Clustal]]W}}
| {{some|[[Neighbor joining|NJ]]}}
| Manual annotation, conservation scores
| [[Nexus file|Nexus]], MSF, [[Clustal]], [[FASTA format|FASTA]], PFAAT
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|pfaat.sourceforge.net}}
|-
| Ralee (emacs plugin for RNA al. editing)
| {{dunno}}
| {{some|RNA structure}}
| {{dunno}}
| {{dunno}}
| [[Stockholm format|Stockholm]]
| {{free}}, [[GNU General Public License|GPL]]
|?
|?
| {{Official website|bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257}}
|-
| S2S RNA editor
| {{some|2D structure}}
| {{some|Rnalign}}
| {{no}}
| Base-base interactions, 2D-3D viewer
| [[FASTA format|FASTA]], RnaML
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|bioinformatics.org/S2S}}
|-
| Seaview
| {{no}}
| {{yes|local MUSCLE-[[Clustal]]W}}
| {{yes|Parsimony, distance methods, PhyML}}
| Dot-plot, [[vim (text editor)|vim]]-like editing keys
| [[Nexus file|Nexus]], MSF, [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP]], [[MASE format|MASE]]
| {{free}}, [[GNU General Public License|GPL]] 3
|?
| Linux, Mac OS, Windows
| {{Official website|pbil.univ-lyon1.fr/software/seaview.html}}
|-
| Seqotron
| {{no}}
| {{yes|[[MUSCLE (alignment software)|MUSCLE]], [[MAFFT]]}}
| {{yes|[[UPGMA]], [[Neighbor joining|NJ]], ML (Physher)}}
| Manual alignment, tree visualisation
| [[Nexus file|Nexus]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP]], [[MEGA, Molecular Evolutionary Genetics Analysis|MEGA]], [[Stockholm format|Stockholm]], NBRF/[[Protein Information Resource|PIR]], GDE flat
| {{free}}, [[GNU General Public License|GPL]]
|?
|Mac OS X
| {{Official website|github.com/4ment/seqotron}} [https://www.ncbi.nlm.nih.gov/pubmed/26887850 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|www.sequilab.org}}
|-
| SeqPup
| {{no}}
| {{dunno}}
| {{dunno}}
| {{dunno}}
| {{dunno}}
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|iubioarchive.bio.net/soft/molbio/seqpup/java/}}
|-
| Sequlator
| {{no}}
| {{some|Pairwise alignment}}
| {{no}}
| easy alignment editing
| MSF
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|sequlator.com}}
|-
| SnipViz
| {{no}}
| {{no}}
| {{no}} (but can display them)
| Pure Javascript and HTML; suitable to integrate in websites
| FASTA, newick
| {{free}}, [[Apache License|Apache]] 2.0
|Yes
|Browsers
| {{Official website|github.com/yeastrc/snipviz}}, [https://pubmed.ncbi.nlm.nih.gov/25056180/ publication]
|-
| Strap
| {{yes|Jnet, NNPREDICT, Coiled coil, 16 different TM-helix}}
| {{yes|15 different methods}}
| {{yes|[[Neighbor joining|NJ]]}}
| Dot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, [[BioJava]]-interface
| MSF, [[Stockholm format|Stockholm]], [[Clustal]]W, [[Nexus file|Nexus]], [[FASTA]], [[Protein Data Bank (file format)|PDB]], Embl, [[GenBank]], [[hssp]], [[Pfam]]
| {{free}}, [[GNU General Public License|GPL]]
|?
|?
| {{Official website|3d-alignment.eu}}
|-
| Tablet
| {{no}}
| {{no}}
| {{no}}
| High-performance graphical viewer for viewing next generation sequence assemblies and alignments.
| [[ACE (genomic file format)|ACE]], AFG, MAQ, SOAP2, [[BAM format|SAM]], [[BAM format|BAM]], [[FASTA format|FASTA]], [[FASTQ format|FASTQ]], [[General feature format|GFF3]]
| {{free}}, [[BSD licenses|BSD]] 2-clause
|?
|?
| {{Official website|ics.hutton.ac.uk/tablet}}
|-
| [[UGENE]]
| {{yes}}
| {{yes|[[MUSCLE (alignment software)|MUSCLE]], Kalign, [[Clustal]]W, ClustalO, ClustalX, [[MAFFT]], [[T-Coffee]], [[Smith–Waterman algorithm]]}}
| {{yes}}
| Many
| [[FASTA format|FASTA]], [[FASTQ format|FASTQ]], [[GenBank]], [[EMBL]], ABIF, SCF, [[Clustal]]W, [[Stockholm format|Stockholm]], Newick, [[Protein Data Bank|PDB]], MSF, GFF
| {{free}}, [[GNU General Public License|GPL]]
|?
|?
| {{Official website|ugene.unipro.ru}}
|-
| VISSA sequence-structure viewer
| {{yes|DSSP secondary structure}}
| {{yes|[[Clustal]]X}}
| {{no}}
| Mapping from sequence to 3D structure
| [[Clustal]], [[FASTA format|FASTA]]
| {{proprietary}}, [[freeware]]
|?
|?
| {{Official website|bioinformatics.burnham.org/liwz/vissa}}
|-
| DNApy
| {{no}}
| {{yes|[[MUSCLE (alignment software)|MUSCLE]]}}
| {{no}}
| Editing of GenBank files, plasmid drawing, ABI chromatograms,
| [[FASTA format|FASTA]], [[FASTQ format|FASTQ]], [[GenBank]]
| {{free}}, [[GNU General Public License|GPL]] 3
|?
|?
| {{Official website|https://github.com/mengqvist/DNApy}}
|-
| Alignment Annotator
| {{yes}}
| {{yes|By sequence or mixed sequence and structure}}
| {{yes|Includes [[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]]}}
| [[Distributed Annotation System|DAS]] and user defined annotations. Scriptable. Export to HTML, Word, [[Jalview]].
| Many
| {{free}}, [[GNU General Public License|GPL]]
|Yes
|iOS, Android, MS-Mobile, 
Browsers
| {{Official website|www.bioinformatics.org/strap/aa}}
|}

==See also==
* [[Sequence alignment software]]
* [[Biological data visualization]]
* [[Comparison of software for molecular mechanics modeling]]

{{DEFAULTSORT:Alignment visualization software}}
[[Category:Lists of bioinformatics software]]
[[Category:Visualization software|Software]]