|
This page is a subsection of the [[Listlist of sequence alignment software]].
Multiple alignment visualization tools typically serve four purposes:
* GeneralAid comprehensiongeneral understanding of large-scale DNA or protein alignments
* Visualization ofVisualize alignments for figures and publication.
* ManualManually editingedit and curation ofcurate automatically generated alignments.
* Analysis in depth
* In depth analysis
The rest of this article is focused on justonly multiple global alignments of homologous proteins. The first two are a natural consequence of the fact that most computational representations of alignments and their annotation are notbeing human readable-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is a necessitynecessary because algorithms for both ''[[Multiplemultiple sequence alignment]]'' and ''[[Structuralstructural alignment]]'' algorithms utiliseuse 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 in order 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"
|-
! Name
! Structure prediction tools integrated
! Integrated with Struct. Prediction Tools
! Can Alignalign Sequencessequences
! Can Calculatecalculate Phylogeneticphylogenetic Treestrees
! Other Featuresfeatures
! Format support
! Formats Supported
! [[Software license|License]]
! Link
|-
| Ale ([[emacs]] plugin)
| No{{no}}
| Yes{{yes}}
| No{{no}}
| No{{no}}
| GenBank, EMBL, Fasta,[[FASTA andformat|FASTA]], Phylip[[PHYLIP]]
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|www.red-bean.com/ale/ link]}}
|-
| AliView 2016
| No{{no}}
| Muscle is{{yes|MUSCLE integrated.; Otherother programs such as MAFFT can be defined.}}
| {{some|External programs such as FastTree can be called from within}}
| Fast, very easy navigation through unlimited mouse wheel zoom in/-out feature. Handles unlimited file size alignments. Degenerate primer design.
| [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[Nexus file|Nexus]], [[MSF format|MSF]] and, [[Clustal]]
| {{free}}, [[GNU General Public License|GPL]] 3
| [[GPL3]]
| [http://{{Official website|www.ormbunkar.se/aliview link]}}
|-
| Base-By-Base
| No{{no}}
| {{yes|MUSCLE}}
| Muscle
| {{yes|UPGMA, [[Neighbor joining|NJ]], Completecomplete Linkage,and Singlesingle Linkagelinkages, WPMGA}}
| Visual summary, percent identity tables, some integrated advanced analysis tools
| Genbank, Fasta[[FASTA format|FASTA]], EMBEL, [[Clustal]], Basebase-by-base files
| {{proprietary}}, [[freeware]], must register
| Free, registration required
| [http://{{Official website|athena.bioc.uvic.ca/virology-ca-tools/base-by-base/ link]}}
|-
| BioEdit
| No{{no}}
| {{yes|[[Clustal]]W}}
| ClustalW
| rudimentary{{some|Rudimentary, can read phylip[[PHYLIP]]}}
| plasmidPlasmid drawing, ABI chromatograms,
| Genbank, Fasta[[FASTA format|FASTA]], Phylip[[PHYLIP]] 3.2, Phylipand 4, NBRF/-PIR
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|www.mbio.ncsu.edu/BioEdit/bioedit.html link]}}
|-
| [[BioNumerics]]
| No{{no}}
| Yes{{yes}}
| Yes{{yes}}
| {{dunno}}
|
| Genbank, Fasta[[FASTA format|FASTA]]
| {{proprietary}}, [[Commercial software|commercial]]
| [http://{{Official website|www.applied-maths.com/bionumerics/bionumerics.htm link]}}
|-
| BoxShade
| No{{no}}
| No{{no}}
| No{{no}}
| Specifically for multiple alignments
| MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq).; ALN format as written by CLUSTALW.[[Clustal]]W
| Public{{free}}, [[public ___domain]]
| [http://{{Official website|ch.embnet.org/software/BOX_form.html link]}}
|-
| CINEMA
| NO{{no}}, but can read/-show 2D structure annotations
| {{yes|[[Clustal]]W}}
| ClustalW
| No{{no}}
| Dotplot, 6 frame translation, Blast
| [[Nexus file|Nexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[PIRProtein formatInformation Resource|PIR]], PRINTS
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|aig.cs.man.ac.uk/research/utopia/cinema/cinema.php link]}}
|-
| CLC viewer (Freefree version)
| {{some|Commercial version only}}
| only in commercial version
| {{yes|[[Clustal]], MuscleMUSCLE, T-Coffee, MAFFT, kalignKalign, various}}
| {{yes|UPGMA, [[Neighbor joining|NJ]]}}
| workflowsWorkflows, blast/-genbank search
| many
| Freeware{{proprietary}}, [[freeware]]. More options available in commercial versions.
| {{Official website|www.clcbio.com}}
| [http://www.clcbio.com/index.php?id=28 link], [http://www.clcbio.com/index.php?id=487 table of features]
|-
| ClustalX[[Clustal]]X viewer
| No{{no}}
| {{yes|[[Clustal]]W}}
| ClustalW
| {{yes|[[Neighbor- joining|NJ]]}}
| Alignment quality analysis
| [[Nexus file|Nexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]]
| Free{{proprietary}}, [[freeware]] for academic usersuse
| [http://{{Official website|www.clustal.org/ link]}}
|-
| Cylindrical BLAST Viewer
| No{{no}}
| No{{no}}
| No{{no}}
| 3D, Animationanimation, Drilldowndrilldown, Legendlegend Selectionselection
| BLAST XML, proprietary XML, GFF3, ClustalW[[Clustal]]W, INSDSet, user expandable with [[XSLT]]
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|sourceforge.net/projects/cyl-viewer/ link]}}
|-
| DECIPHER
| Yes{{yes}}
| Yes{{yes}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], ML}}
| Primer/-Probe design, Chimera finding
| FASTA, FASTQ, GenBank
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|decipher.cee.wisc.edu/Download.html link]}}
|-
| Discovery Studio
| Yes{{yes}}
| {{yes|Align123, ClustalW[[Clustal]]W, S-ALIGN}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], with bootstrap and best tree}}
| Visualizer supports 2D and 3D structure and sequence.; Full featuredfull version has comprehensive functionality for Proteinprotein, nucleotides and, more.
| BSML, EMBL, GB, HELM, [[Clustal]], [[FASTA]], GDE, [[Protein Data Bank (file format)|PDB]], SEQ, SPT, ...
| {{proprietary}}, [[Commercial software|commercial]], Viewer is [[Freeware]]
| Viewer is free for everyone
| [http://{{Official website|accelrys.com/products/discovery-studio/visualization-download.php link]}}
|-
| DnaSP
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| canCan compute several population genetics statistics, reconstruct haplotypes with PHASE
| [[FASTA]], [[Nexus file|Nexus]], MegaMEGA, [[PHYLIP]]
| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for noncomercial use
| [[Freeware]]
| [http://{{Official website|www.ub.es/dnasp/ link]}}
|-
| [[DNASTAR]] Lasergene Molecular Biology Suite
| Yes{{yes}}
| Yes{{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, and translation.
| ABI, DNA Multi-Seq, [[FASTA format|FASTA]], GCG Pileup, GenBank, Phred
| {{proprietary}}, [[Commercial software|commercial]], Academicacademic licenses available
| [https://{{Official website|www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx link]}}
|-
| [[emacs]] - biomode
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| {{free}}, [[GNU General Public License|GPL]]
|
| [http://packages{{Official website|archive.debian.orgnet/testing/sciencelenny/biomode link]}}
|-
| FLAK
| No{{no}}
| Yes. {{some|Can perform a fuzzy whole genome alignment}}
| No.{{no}}
| Very fast and, highly customisable., Visualisationvisualisation is WYSIWYG with filtering and fuzzy options.
| FASTA
| Free{{proprietary}}, [[Commercial software|commercial]], [[freeware]] for noncommercial use
| [http://{{Official website|flakbio.com/index.html link]}}
|-
| Genedoc
| No{{no}}, but can read/-show annotations
| {{some|Pairwise}}
| No{{no}}, but can read/-show annotations
| gel simulation, stats, multiple views, simple
| many
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|www.nrbsc.org/gfx/genedoc/ link]}} [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features]
|-
| [[Geneious]]
| Yes{{yes}} - powered by [[EMBOSS]] tools
| {{yes|[[Clustal]], MuscleMUSCLE, MAUVE, profile, translation}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], PhyML, MrBayes plugin, PAUP* plugin}}
| Whole genome assembly, restriction analysis, cloning, primer design, dotplot and, much more
| >40 file formats imported and exported
| {{proprietary}}, [[Commercial software|commercial]]; personal, floating
| Personal and Floating
| [http://{{Official website|www.geneious.com link]}}
|-
| [[Integrated Genome Browser]] (IGB)
| No{{no}}
| No{{no}}
| No{{no}}
| sequencesSequences and features from files, URLs, and arbitrary [[Distributed Annotation System|DAS]] and QuickLoad servers
| BAM, [[FASTA format|FASTA]], PSL
| {{free}}, [[Common Public License|CPL]]
| [http://{{Official website|igb.bioviz.org link]}}
|-
| interactive Tree Of Life (iTOL)
| No{{no}}
| 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 the alignments.
| FASTA
| {{proprietary}}, free use
| Free
| {{Official website|itol.embl.de}}
| [http://itol.embl.de link] [http://itol.embl.de/help.cgi#alignment manual]
|-
| IVisTMSA
| [[IVistMSA]]
| No{{no}}
| {{yes|[[Clustal]] Omega, ClustalW2, MAFFT, MUSCLE, and [[BioJava]] have beenare integrated forto constructingconstruct alignment}}
| {{yes|Tree calculation tool calculates a phylogenetic tree using BioJava API and permits thelets user to draw the treetrees using [[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]]}}
|IVisTMSA Software is a software package of seven7 interactive visual tools for multiple sequence alignments. Major focus is on manipulating large alignments. It includesIncludes MSApad, MSA comparator, MSA reconstruction tool, [[FASTA format|FASTA]] generator and MSA ID matrix calculator
|ClustalW [[Clustal]]W, MSF, Phylip[[PHYLIP]], [[Protein Information Resource|PIR]], GDE, and Nexus
| {{proprietary}}, [[freeware]]
|Free
| [http://{{Official website|www.ivistmsa.com/ link]}}
|-
| Jalview 2
| {{yes|Secondary Struct.structure Predictionprediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JNET]}}
| {{yes|[[Clustal]], MuscleMUSCLE, MAFFT, Probcons, TCoffee via web services}}
| {{yes|UPGMA, [[Neighbor joining|NJ]]}}
| sequencesSequences and features from arbitrary and publicly registered [[Distributed Annotation System|DAS]] servers, PFAM, PDB, EMBL and, Uniprot Accession retrieval.
| [[FASTA format|FASTA]], [[PFAM format|PFAM]], [[MSF format|MSF]], [[Clustal]], [[BLC format|BLC]], [[PIRProtein formatInformation Resource|PIR]], [[Stockholm format|Stockholm]]
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|www.jalview.org/ link]}}
|-
| Jevtrace
| JEvTrace
| No but integrated{{some|Integrated with structure viewer [http://www.cmpharm.ucsf.edu/~walther/webmol.html WebMol]}}
| No{{no}}
| No{{no}}
| A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive [http://www.ncbi.nlm.nih.gov/pubmed/8609628 Evolutionary Trace] and other phylogeny inspired analysis.
| [[FASTA format|FASTA]], MSF, [[Clustal]], [[PHYLIP format|PHYLIP]], [[Newick format|Newick]], [[Protein Data Bank (file format)|PDB]]
| {{proprietary}}, [[FreeCommercial software|commercial]], [[freeware]] for academic use]]
| [http://{{Official website|compbio.berkeley.edu/people/marcin/jevtrace/ link]}} [http://compbio.berkeley.edu/people/marcin/jevtrace/jevtracev3.12_manual.pdf manual]
|-
| JSAV
| No{{no}}
| No{{no}}
| No{{no}}
| A JavaScript component allowing integration ofintegrating an alignment viewer into web pages.
| An array of JavaScript objects
| {{free}}, [[GNU General Public License|GPL]] 2
| [[GPL2]]
| [http://{{Official website|www.bioinf.org.uk/software/jsav/ link]}}
|-
| Maestro
| Yes{{yes}}
| {{yes|[[Clustal]]X}}
| ClustalX
| Yes{{yes}}
| Mapping from sequence to 3D structure, structure/-sequence editing/-modeling
| [[Clustal]], [[FASTA format|FASTA]] [[Protein Data Bank|PDB]]
| {{proprietary}}, [[freeware]] for academic use
| Free for Academics
| [http://{{Official website|www.schrodinger.com/products/14/12/ link]}}
|-
| [[MEGA,_Molecular_Evolutionary_Genetics_Analysis Molecular Evolutionary Genetics Analysis|MEGA]]
| No{{no}}
| {{yes|Native ClustalW[[Clustal]]W}}
| {{yes|UPGMA, [[Neighbor joining|NJ]], ME, MP, with bootstrap and confidence test}}
| extendedExtended support to phylogenetics analysis
| FASTA, [[Clustal]], Nexus, MegaMEGA, etc..
| {{proprietary}}, [[freeware]], must register
| Freeware, registration requested
| [http://www.megasoftware.net/{{Official link], [http://website|www.megasoftware.net/features.html table of features]}}
|-
| MSAReveal.org
| {{no}}
|No
| {{no}}
|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 {{free}}, open[[Creative source,Commons license|Creative Commons]] Attribution NonCommercial ShareAlike[[Share-alike]]
|[http://msareveal.org link]{{Official [http://website|msareveal.org/help.html features]}}
|-
| Multiseq ([[Visual Molecular Dynamics|vmdVMD]] plugin)
| No{{no}}, but can display and align 3D structures
| ClustalW{{yes|[[Clustal]]W, MAFFT, Stamp (Structural)}}
| {{yes|Percent identity, [[Clustal]], MAFFT, Structural}}
| Scripting via [[Tcl]], mapping from sequence to 3D structure
| FASTA, PDB, ALN, PHYLYP[[PHYLIP]], NEXUS
| Free{{proprietary}}, [[freeware]], but VMD is free only for noncommercial use only
| [http://{{Official website|www.scs.illinois.edu/schulten/multiseq/ link]}}
|-
| MView
| No{{no}}
| No{{no}}
| No{{no}}
| stackedStacked 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]]
| [[GPL]]
| [http://{{Official website|bio-mview.sourceforge.net link]}}
|-
| PFAAT
| NO{{no}}, but can display 3D structures
| {{yes|[[Clustal]]W}}
| ClustalW
| {{some|[[Neighbor- joining|NJ]]}}
| Manual annotation, conservation scores
| [[Nexus file|Nexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], PFAAT
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|pfaat.sourceforge.net/ link]}}
|-
| Ralee (emacs plugin for RNA al. editing)
| {{dunno}}
|
| {{some|RNA structure}}
| {{dunno}}
|
| {{dunno}}
|
| [[Stockholm format|Stockholm]]
| {{free}}, [[GNU General Public License|GPL]]
|[[GPL]]
| [http://{{Official website|bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257 link]}}
|-
| S2S RNA editor
| {{some|2D structure}}
| {{some|Rnalign}}
| No{{no}}
| baseBase-base interactions, 2D,-3D viewer
| [[FASTA format|FASTA]], RnaML
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|bioinformatics.org/S2S/ link]}}
|-
| Seaview
| No{{no}}
| {{yes|local Muscle/ClustalWMUSCLE-[[Clustal]]W}}
| {{yes|Parsimony, distance methods, PhyML}}
| Dot-plot, [[vim (text editor)|vim]]-like editing keys
| [[Nexus file|Nexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[MASE format|MASE]]
| {{proprietary}}, [[freeware]]
|
| [http://{{Official website|pbil.univ-lyon1.fr/software/seaview.html link]}}
|-
| Seqotron
| No{{no}}
| {{yes|[[Multiple Sequence ComparisonMUSCLE by(alignment Log-Expectationsoftware)|MUSCLE]], [[MAFFT]]}}
| {{yes|[[UPGMA]], [[Neighbor- joining|NJ]], ML (Physher)}}
| Manual alignment, tree visualisation.; Runsruns on Mac [[OS X.]]
| [[Nexus file|Nexus]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[MEGA,_Molecular_Evolutionary_Genetics_Analysis Molecular Evolutionary Genetics Analysis|MEGA]], [[Stockholm format|Stockholm]], NBRF/[[Protein Information Resource|PIR]], GDE flat
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [https://{{Official website|github.com/4ment/seqotron link]}} [http://www.ncbi.nlm.nih.gov/pubmed/26887850 publication]
|-
| Sequilab
| Yes{{yes}}
| Yes{{yes}}
| No{{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]], DragNdropdrag-drop from external [[URL]] from within the user interface
| {{proprietary}}, [[freeware]]
| [[Freeware]]
| [http://{{Official website|www.sequilab.org/ link]}}
|-
| SeqPop
| No{{no}}
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| {{dunno}}
|
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|iubio.bio.indiana.edu/soft/molbio/seqpup/java/ link]}}
|-
| Sequlator
| No{{no}}
| {{some|Pairwise alignment}}
| No{{no}}
| easy alignment editing
| [[MSF format|MSF]]
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|sequlator.com link]}}
|-
| SnipViz
| No{{no}}
| No{{no}}
| No{{no}} (but can display them)
| Pure Javascript and HTML.; Suitablesuitable forto integrationintegrate intoin web sites.websites
| FASTA, newick
| {{free}}, [[Apache License|Apache]] 2.0
| [https://{{Official website|github.com/yeastrc/snipviz link]}}, [http://www.ncbi.nlm.nih.gov/pubmed/?term=25056180 publication]
|-
| Strap
| {{yes|Jnet, NNPREDICT, Coiled coil, 16 different TM-helix}}
| Fifteen{{yes|15 different Methodsmethods}}
| {{yes|[[Neighbor- joining|NJ]]}}
| Dot-plot, Structurestructure-neighbors, 3D-superposition, Blast-search, Mutation/-SNP analysis, Sequence features, [[BiojavaBioJava]]-interface
| [[MSF format|MSF]], [[Stockholm format|Stockholm]], [[Clustal]]wW, [[Nexus file|Nexus]], [[FASTA]], [[Protein Data Bank (file format)|PDB]], Embl, [[GenBank]], [[hssp]], [[Pfam]]
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|3d-alignment.eu/ link]}}
|-
| Tablet
| No{{no}}
| No{{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]], and [[General feature format|GFF3]]
| {{free}}, [[BSD licenses|BSD]] 2-clause
| [http://ics.hutton.ac.uk/tablet/download-tablet/tablet-licence/ Open source, (c)James Hutton Institute]
| [http://{{Official website|ics.hutton.ac.uk/tablet/ link]}}
|-
| [[UGENE]]
| Yes{{yes}}
| {{yes|[[MultipleMUSCLE Sequence(alignment Comparison by Log-Expectationsoftware)|MUSCLE]], [[KAlign]]Kalign, [[Clustal]]W, [[Clustal]]OClustalO, [[Clustal]]XClustalX, [[MAFFT]], [[T-Coffee]], [[Smith–Waterman algorithm|Smith-Waterman algorithm]]}}
| Yes{{yes}}
| manyMany
| [[FASTA format|FASTA]], [[FASTQ format|FASTQ]], [[GenBank]], [[EMBL]], ABIF, SCF, [[Clustal|CLUSTALW]]W, [[Stockholm format|Stockholm]], Newick, [[Protein Data Bank|PDB]], MSF, GFF
| {{free}}, [[GNU General Public License|GPL]]
| [[GPL]]
| [http://{{Official website|ugene.unipro.ru link]}}
|-
| VISSA sequence/-structure viewer
| {{yes|DSSP secondary structure}}
| {{yes|[[Clustal]]X}}
| ClustalX
| No{{no}}
| Mapping from sequence to 3D structure
| [[Clustal]], [[FASTA format|FASTA]]
| {{proprietary}}, [[freeware]]
| Free
| [http://{{Official website|bioinformatics.burnham.org/liwz/vissa/ link]}}
|-
| [[DNApy]]
| No{{no}}
| {{yes|[[MUSCLE (alignment software)|MUSCLE]]}}
| No{{no}}
| Editing of GenBank files, plasmid drawing, ABI chromatograms,
| [[FASTA format|FASTA]], [[FASTQ format|FASTQ]], [[GenBank]]
| {{free}}, [[GNU General Public License|GPL]] 3
| [[GPL3]]
| [http://{{Official website|DNApy.org link]}}
|-
| Alignment Annotator
| Yes{{yes}}
| {{yes|By sequence or mixed sequence and structure}}
| {{yes|Includes [[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]] }}
| Running in modern web browsers of desktop PCs +, tablets (iOS, Android, MS-Mobile). [[Distributed Annotation System|DAS]] and user defined annotations. Scriptable. Export to HTML, Word and, [[Jalview]].
| Many
| {{free}}, [[GNU General Public License|GPL]]
| GPL
| [http://{{Official website|www.bioinformatics.org/strap/aa/ link]}}
|
|}
* [[Sequence alignment software]]
* [[Biological data visualization]]
* [[ListComparison of software for molecular mechanics modeling]]
{{DEFAULTSORT:Alignment visualization software}}
| 