List of alignment visualization software: Difference between revisions

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

This page is a subsection of the [[list 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 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]]

!Can run on Browser

!Operating Platforms

! Link

|-

| Alan

| Ale (emacs plugin)

| No{{no}}

| Yes{{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

| No

| {{Official website|https://pypi.org/project/alv/}}, see also {{GitHub|https://github.com/arvestad/alv}}

| GenBank, EMBL, Fasta, and Phylip

| [[GPL]]

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

|-

| [[ARB_Project|arb]]

| AliView 2016

| {{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)

| Muscle is integrated. Other programs such as MAFFT can be defined.

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

| 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]]

| [[GPL3]]

| [http://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://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/ link]

|?

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

|-

| 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

|No

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

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

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

|-

| [[BioNumerics]]

| No{{no}}

| Yes{{yes}}

| Yes{{yes}}

| {{dunno}}

|

| Genbank, Fasta[[FASTA format|FASTA]]

| {{proprietary}}, [[Commercial software|commercial]]

|?

| [http://www.applied-maths.com/bionumerics/bionumerics.htm link]

|?

| {{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{{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]]

|No

| [http://ch.embnet.org/software/BOX_form.html link]

|MSDOS, VMS

| {{Official website|ch.embnet.org/software/BOX_form.html}}

|-

| 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

|No

| [http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php link]

|Cross-platform -Mac OS, Linux, Windows

| {{Official website|aig.cs.man.ac.uk/research/utopia/cinema/cinema.php}}

|-

| 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.

|No

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

|?

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

|-

| CIAlign

| ClustalX viewer

| {{no}}

| {{no}}

| {{no}}

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

| [[FASTA format|FASTA]]

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

| No

| Linux, Windows, MacOS

| ClustalW

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

| [[Neighbor-joining]]

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

|-

| [[Clustal]]X viewer

| {{no}}

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

| {{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

|No

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

|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{{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://sourceforge.net/projects/cyl-viewer/ link]

|?

| {{Official website|sourceforge.net/projects/cyl-viewer}}

|-

| 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]]

|No

| [http://decipher.cee.wisc.edu/Download.html link]

|Mac OS, Windows

| {{Official website|decipher.cee.wisc.edu/Download.html}}

|-

| 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://accelrys.com/products/discovery-studio/visualization-download.php link]

|Linux, Windows

| {{Official website|accelrys.com/products/discovery-studio/visualization-download.php}}

|-

| 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 noncommercial use

| [[Freeware]]

|?

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

|Cross-platform -Mac OS, Linux, Windows

| {{Official website|www.ub.es/dnasp}}

|-

| [[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://www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx link]

|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]]

|

|?

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

|?

| {{Official website|archive.debian.net/lenny/biomode}}

|-

| 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://flakbio.com/index.html link]

|?

| {{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]

|-

| [[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://www.geneious.com link]

|Cross-platform - Mac, Windows, Linux

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

|-

| [[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://igb.bioviz.org link]

|Cross-platform - Mac, Windows, Linux

| {{Official website|igb.bioviz.org}}

|-

| 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

|Yes

| [http://itol.embl.de link] [http://itol.embl.de/help.cgi#alignment manual]

|Browser

| {{Official website|itol.embl.de}}

|-

| 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://www.ivistmsa.com/ link]

|?

| www.ivistmsa.com

|-

| [[Jalview 2]]

| {{yes|Secondary Struct.structure Predictionprediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JNETJPred 4]}}

| {{yes|[[Clustal#Clustal_Omega|Clustal O]], Muscle[[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]].

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

| [[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]].

| [[FASTA format|FASTA]], [[PFAM format|PFAM]], [[MSF format|MSF]], [[Clustal]], [[BLC format|BLC]], [[PIR format|PIR]], [[Stockholm format|Stockholm]]

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

| [[GPL]]

| [httphttps://www.jalview.org/jalview-js/ linkJalviewJS] (Javascript)

|Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine.

| {{Official website|https://www.jalview.org/}}

|-

| 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 [httphttps://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://compbio.berkeley.edu/people/marcin/jevtrace/ link] [http://compbio.berkeley.edu/people/marcin/jevtrace/jevtracev3.12_manual.pdf manual]

|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{{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]]

|Yes

| [http://www.bioinf.org.uk/software/jsav/ link]

|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}}

| {{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://www.schrodinger.com/products/14/12/ link]

|?

| {{Official website|www.schrodinger.com/products/14/12}}

|-

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

|?

| {{Official website|www.megasoftware.net}}

|-

| [[Molecular Operating Environment]] (MOE)

|MSAReveal.org

| {{yes}}

|No

| {{yes}}

|No

| {{yes}}

|No

| Part of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc.

|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.

| [[Clustal]], [[FASTA format|FASTA]], [[Protein Data Bank|PDB]], EMBL, GCG, GCG_MSF, Genbank, [[PHYLIP]], [[Protein Information Resource|PIR]], raw_seq

|FASTA

| {{proprietary}}

|Free, open source, Creative Commons Attribution NonCommercial ShareAlike

|?

|[http://msareveal.org link] [http://msareveal.org/help.html features]

|?

| {{Official website|www.chemcomp.com/MOE-Molecular_Operating_Environment.htm}}

|-

| MSAReveal.org

| Multiseq ([[Visual Molecular Dynamics|vmd]] plugin)

| {{no}}

| No, but can display and align 3D structures

| {{no}}

| ClustalW, MAFFT, Stamp (Structural)

| {{no}}

| Percent identity, Clustal, MAFFT, Structural

| 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, PHYLYP[[PHYLIP]], NEXUS

| Free{{proprietary}}, [[freeware]], but VMD is free only for noncommercial use only

|?

| [http://www.scs.illinois.edu/schulten/multiseq/ link]

|?

| {{Official website|www.scs.illinois.edu/schulten/multiseq}}

|-

| 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]]

|No

| [http://bio-mview.sourceforge.net link]

|Cross-platform - Mac OS, Linux, Windows

| {{Official website|desmid.github.io/mview}}

|-

| 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://pfaat.sourceforge.net/ link]

|?

| {{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}}

|-

| S2S RNA editor

| {{some|2D structure}}

| {{some|Rnalign}}

| No{{no}}

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

| [[FASTA format|FASTA]], RnaML

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

| Free

|?

| [http://bioinformatics.org/S2S/ link]

|?

| {{Official website|bioinformatics.org/S2S}}

|-

| 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]]

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

|

|?

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

| Linux, Mac OS, Windows

| {{Official website|pbil.univ-lyon1.fr/software/seaview.html}}

|-

| Seqotron

| No{{no}}

| {{yes|[[Multiple Sequence ComparisonMUSCLE by(alignment Log-Expectationsoftware)|MUSCLE]], [[MAFFT]]}}

| {{yes|[[UPGMA]], [[Neighbor- joining|NJ]], ML (Physher)}}

| Manual alignment, tree visualisation. Runs 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://github.com/4ment/seqotron link] [http://www.ncbi.nlm.nih.gov/pubmed/26887850 publication]

|Mac OS X

| {{Official website|github.com/4ment/seqotron}} [https://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://www.sequilab.org/ link]

|?

| {{Official website|www.sequilab.org}}

|-

| SeqPopSeqPup

| No{{no}}

| {{dunno}}

|

| {{dunno}}

|

| {{dunno}}

|

| {{dunno}}

|

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

| Free

|?

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

|?

| {{Official website|iubioarchive.bio.net/soft/molbio/seqpup/java/}}

|-

| Sequlator

| No{{no}}

| {{some|Pairwise alignment}}

| No{{no}}

| easy alignment editing

| [[MSF format|MSF]]

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

| Free

|?

| [http://sequlator.com link]

|?

| {{Official website|sequlator.com}}

|-

| 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

|Yes

| [https://github.com/yeastrc/snipviz link] [http://www.ncbi.nlm.nih.gov/pubmed/?term=25056180 publication]

|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}}

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

|?

| {{Official website|3d-alignment.eu}}

|-

| 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://ics.hutton.ac.uk/tablet/ link]

|?

| {{Official website|ics.hutton.ac.uk/tablet}}

|-

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

|?

| {{Official website|ugene.unipro.ru}}

|-

| 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://bioinformatics.burnham.org/liwz/vissa/ link]

|?

| {{Official website|bioinformatics.burnham.org/liwz/vissa}}

|-

| [[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://DNApy.org link]

|?

| {{Official website|https://github.com/mengqvist/DNApy}}

|-

| 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

|Yes

| [http://www.bioinformatics.org/strap/aa/ link]

|iOS, Android, MS-Mobile,

|

Browsers

| {{Official website|www.bioinformatics.org/strap/aa}}

|}

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

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

==See also==

* [[Sequence alignment software]]

* [[Biological data visualization]]

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

{{DEFAULTSORT:Alignment visualization software}}

[[Category:BioinformaticsLists of bioinformatics software]]

[[Category:Visualization (graphic)software|Software]]

[[Category:Lists of software]]