List of alignment visualization software: Difference between revisions

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{{Short description|none}}

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

Multiple alignment visualization tools typically serve four purposes:

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

* 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.

Multiple alignment visualization tools typically serve three purposes:

== Alignment viewers, editors ==

* Visualization of alignments for figures and publication.

{| class="wikitable sortable"

* Manual editing and curation of automatically generated alignments.

|-

* In depth analysis

The first is a natural consequence of the fact that most computational representations of alignments and their annotation are not human readable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The second is a necessity because both [[Multiple sequence alignment]] and multiple [[Structure alignment]] algorithms utilise heuristics which do not always perform perfectly. The third 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]]

! 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]]