List of alignment visualization software: Difference between revisions

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{{Short description|none}}

Multiple alignment visualization tools typically serve three purposes:

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

Multiple alignment visualization tools typically serve four purposes:

* Visualization of alignments for figures and publication.

* ManualAid editinggeneral and curationunderstanding of automaticallylarge-scale DNA or generatedprotein alignments.

* Visualize alignments for figures and publication

* In depth analysis

* Manually edit and curate automatically generated alignments

* Analysis in depth

The firstrest of this article is afocused naturalon consequenceonly multiple global alignments of thehomologous factproteins. thatThe mostfirst computationaltwo are a natural consequence of most 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 secondthird is a necessitynecessary because algorithms for both ''[[Multiplemultiple sequence alignment]]'' and multiple ''[[Structurestructural alignment]]'' algorithms utiliseuse heuristics which do not always perform perfectly. The thirdfourth 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/Editorsviewers, editors ==

{| class="wikitable sortable"

|-

! 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]]

! License

!Can run on Browser

!Operating Platforms

! Link

!

|-

| DnaSPAlan

| {{no}}

| {{no}}

| {{no}}

| Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding

| can compute several population genetics statistics, reconstruct haplotypes with PHASE

| [[FASTA]], [[NEXUSformat|FASTA]], Mega, [[PHYLIPClustal]]

| {{free}}, [[GNU General Public License|GPL]] 3

| [[Freeware]]

|No

| [http://www.ub.es/dnasp/ link]

|Linux Terminal

| {{Official website|https://github.com/mpdunne/alan}}

|-

| Ale ([[emacs]] plugin)

| Strap

| {{no}}

| Jnet, NNPREDICT, Coiled coil, 16 different TM-helix

| {{yes}}

| Fifteen different Methods

| {{no}}

| [[Neighbor-joining]]

| {{no}}

| Dot-plot, Structure-neighbors, 3D-superposition, Blast-search, Mutation/SNP analysis, Sequence features, [[Biojava]]-interface

| [[MSF]]GenBank, EMBL, [[StockholmFASTA format|Stockholm]], [[Clustal]]w, Nexus, [[FASTA]], [[PDB]], Embl, [[GenBank]], [[hssp]], [[PfamPHYLIP]]

| {{free}}, [[GNU General Public License|GPL]]

| [[GPL]]

|No

| [http://3d-alignment.eu/ link]

|GNU Emacs

| {{Official website|www.red-bean.com/ale}}

|-

| AliView 2025

| Seaview

| {{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

| local Muscle/Clustalw

| {{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)

| Dot-plot, [[vim]]-like editing keys

| {{Official website|http://www.arb-home.de/}}

| [[Nexus format|NEXUS]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[MASE format|MASE]]

|

| [http://pbil.univ-lyon1.fr/software/seaview.html link]

|-

| Base-By-Base

| Jalview 2

| {{no}}

| Secondary Struct. Prediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JNET]

| {{yes|MUSCLE}}

| Clustal, Muscle, MAFFT via web services

| {{yes|UPGMA, [[Neighbor joining|NJ]], complete and single linkages, WPMGA}}

| UPGMA, NJ

| Visual summary, percent identity tables, some integrated advanced analysis tools

| sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL and Uniprot Accession retrieval.

| Genbank, [[FASTA format|FASTA]], [[PFAM format|PFAM]], [[MSF format|MSF]]EMBEL, [[Clustal]], [[BLCbase-by-base format|BLC]], [[PIR format|PIR]], [[Stockholm format|Stockholm]]files

| {{proprietary}}, [[freeware]], must register

| [[GPL]]

|?

| [http://www.jalview.org/ link]

|?

| {{Official website|athena.bioc.uvic.ca/virology-ca-tools/base-by-base}}

|-

| BioEdit

| CLC viewer (Free version)

| {{no}}

| only in commercial version

| {{yes|[[Clustal]]W}}

| Clustal, Muscle, T-Coffee, MAFFT, kalign, various

| {{some|Rudimentary, can read [[PHYLIP]]}}

| UPGMA, NJ

| Plasmid drawing, ABI chromatograms,

| workflows, blast/genbank search

| Genbank, [[FASTA format|FASTA]], [[PHYLIP]] 3.2 and 4, NBRF-PIR

| many

| {{proprietary}}, [[freeware]]

| Freeware. More options available in commercial versions.

|No

| [http://www.clcbio.com/index.php?id=28 link], [http://www.clcbio.com/index.php?id=487 table of features]

|Windows (95/98/NT/2000/XP)

| {{Official website|www.mbio.ncsu.edu/BioEdit/bioedit.html}}

|-

| [[UGENEBioNumerics]]

| No{{no}}

| {{yes}}

| [[MUSCLE]]

| No{{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.

| [[FASTA format | FASTA]], [[GenBank]], [[EMBL]], ABIF, SCF, [[Clustal |CLUSTALW]], [[Stockholm format|Stockholm]], Newick, [[Protein Data Bank | PDB]]

|No

| [[GPL]]

|?

| [http://ugene.unipro.ru link]

| {{Official website|www.clcbio.com}}

|-

| MegaCIAlign

| {{no}}

| {{no}}

| {{no}}

| Alignment visualisation as publication-ready images, alignment cleaning.

| [[FASTA format|FASTA]]

| {{free}}, [[MIT License|MIT]]

| No

| Linux, Windows, MacOS

| Native ClustalW

| {{Official website|https://github.com/KatyBrown/CIAlign}}

| UPGMA, NJ, ME, MP, with bootstrap and confidence test

[[doi:10.7717/peerj.12983|Publication]]

| extended support to phylogenetics analysis

|-

| FASTA, Clustal, Nexus, Mega, etc..

| [[Clustal]]X viewer

| Freeware, registration requested

| {{no}}

| [http://www.megasoftware.net/ link], [http://www.megasoftware.net/features.html table of features]

| {{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{{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://www.nrbsc.org/gfx/genedoc/ link] [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features]

|- ?

| {{Official website|www.nrbsc.org/gfx/genedoc}} [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features]

| SeqPop

| No

|

|

|

|

| Free

| [http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/ link]

|-

| Geneious

| BioEdit

| {{yes}} - powered by [[EMBOSS]] tools

| No

| {{yes|[[Clustal]], MUSCLE, MAUVE, profile, translation}}

| ClustalW

| {{yes|UPGMA, [[Neighbor joining|NJ]], PhyML, MrBayes plugin, PAUP* plugin}}

| rudimentary, can read phylip

| Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more

| plasmid drawing, ABI chromatograms,

| >40 file formats imported and exported

| Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR

| {{proprietary}}, [[Commercial software|commercial]]; personal, floating

| Free

|?

| [http://www.mbio.ncsu.edu/BioEdit/bioedit.html link]

|Cross-platform - Mac, Windows, Linux

| {{Official website|www.geneious.com}}

|-

| [[Integrated Genome Browser]] (IGB)

| Ale (emacs plugin)

| No{{no}}

| Yes {{no}}

| No{{no}}

| Sequences and features from files, URLs, and arbitrary [[Distributed Annotation System|DAS]] and QuickLoad servers

| No

| BAM, [[FASTA format|FASTA]], PSL

| GenBank, EMBL, Fast-A, and Phylip

| {{free}}, [[Common Public License|CPL]]

| [[GPL]]

|?

| [http://www.red-bean.com/ale/ link]

|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]]

|[[GPL]]

|?

| [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257 link]

|?

| {{Official website|bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257}}

|-

| emacsS2S -RNA biomodeeditor

| {{some|2D structure}}

|

| {{some|Rnalign}}

|

| {{no}}

|

| Base-base interactions, 2D-3D viewer

|

| [[FASTA format|FASTA]], RnaML

|

| {{proprietary}}, [[freeware]]

|

|?

| [http://packages.debian.org/testing/science/biomode link]

|?

| {{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==

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

* [[Sequence alignment software]]

* http://lists.open-bio.org/pipermail/emboss/2008-July/003324.html

* [[Biological data visualization]]

* [[Comparison of software for molecular mechanics modeling]]

{{DEFAULTSORT:Alignment visualization software}}

[[Category:Lists of bioinformatics software]]

[[Category:Visualization software|Software]]