List of alignment visualization software

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

Multiple alignment visualization tools typically serve four purposes:

• General comprehension of large-scale DNA or protein alignments
• Visualization of alignments for figures and publication.
• Manual editing and curation of automatically generated alignments.
• In depth analysis

The rest of this article is focused on just 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 not human readable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is a necessity because both Multiple sequence alignment and Structural alignment algorithms utilise 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

Name	Integrated with Struct. Prediction Tools	Can Align Sequences	Can Calculate Phylogenetic Trees	Other Features	Formats Supported	License	Link
Ale (emacs plugin)	No	Yes	No	No	GenBank, EMBL, Fasta, and Phylip	GPL	link
AliView	No	Muscle is integrated. Other programs such as MAFFT can be defined.	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, PHYLIP, Nexus, MSF and Clustal	GPL3	link
Base-By-Base	No	Muscle	UPGMA, NJ, Complete Linkage, Single Linkage, WPMGA	Visual summary, percent identity tables, some integrated advanced analysis tools	Genbank, Fasta, EMBEL, Clustal, Base-by-base files	Free, registration required	link
BioEdit	No	ClustalW	rudimentary, can read phylip	plasmid drawing, ABI chromatograms,	Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR	Free	link
BioNumerics	No	Yes	Yes		Genbank, Fasta	Commercial	link
BoxShade	No	No	No	Specifically for multiple alignments	MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq). ALN format as written by CLUSTALW.	Public domain	link
CINEMA	NO, but can read/show 2D structure annotations	ClustalW	No	Dotplot, 6 frame translation, Blast	Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS	Free	link
CLC viewer (Free version)	only in commercial version	Clustal, Muscle, T-Coffee, MAFFT, kalign, various	UPGMA, NJ	workflows, blast/genbank search	many	Freeware. More options available in commercial versions.	link, table of features
ClustalX viewer	No	ClustalW	Neighbor-joining	Alignment quality analysis	Nexus, MSF, Clustal, FASTA, PHYLIP	Free for academic users	link
Cylindrical BLAST Viewer	No	No	No	3D, Animation, Drilldown, Legend Selection	BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT	GPL	link
DECIPHER	No	Yes	UPGMA, NJ, ML	Primer/Probe design, Chimera finding	FASTA, FASTQ, GenBank	GPL	link
Discovery Studio	Yes	Align123, ClustalW, S-ALIGN	UPGMA, NJ, with bootstrap and best tree	Visualizer supports 2D and 3D structure and sequence. Full featured version has comprehensive functionality for Protein, nucleotides and more.	BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT,...	Viewer is free for everyone	link
DnaSP				can compute several population genetics statistics, reconstruct haplotypes with PHASE	FASTA, Nexus, Mega, PHYLIP	Freeware	link
emacs - biomode							link
Genedoc	No, but can read/show annotations	Pairwise	No, but can read/show annotations	gel simulation, stats, multiple views, simple	many	Free	link table of features
Geneious	Yes - powered by EMBOSS tools	Clustal, Muscle, MAUVE, profile, translation	UPGMA, NJ, PhyML, MrBayes plugin, PAUP* plugin	Whole genome assembly, restriction analysis, cloning, primer design, dotplot and much more	>40 file formats imported and exported	Personal and Floating	link
Integrated Genome Browser (IGB)	No	No	No	sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers	BAM, FASTA, PSL	CPL	link
Jalview 2	Secondary Struct. Prediction via JNET	Clustal, Muscle, MAFFT, Probcons, TCoffee via web services	UPGMA, NJ	sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL and Uniprot Accession retrieval.	FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm	GPL	link
JEvTrace	No but integrated with structure viewer WebMol	No	No	A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.	FASTA, MSF, Clustal, PHYLIP, Newick, PDB	Free for academic use	link manual
JSAV	No	No	No	A JavaScript component allowing integration of an alignment viewer into web pages.	An array of JavaScript objects	GPL2	link
Maestro	Yes	ClustalX	Yes	Mapping from sequence to 3D structure, structure/sequence editing/modeling	Clustal, FASTA PDB	Free for Academics	link
MEGA	No	Native ClustalW	UPGMA, NJ, ME, MP, with bootstrap and confidence test	extended support to phylogenetics analysis	FASTA, Clustal, Nexus, Mega, etc..	Freeware, registration requested	link, table of features
Multiseq (vmd plugin)	No, but can display and align 3D structures	ClustalW, MAFFT, Stamp (Structural)	Percent identity, Clustal, MAFFT, Structural	Scripting via Tcl, mapping from sequence to 3D structure	FASTA, PDB, ALN, PHYLYP, NEXUS	Free, but VMD is free only for noncommercial use	link
MView	No	No	No	stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns	BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF	GPL	link
PFAAT	NO, but can display 3D structures	ClustalW	Neighbor-joining	Manual annotation, conservation scores	Nexus, MSF, Clustal, FASTA, PFAAT	Free	link
Ralee (emacs plugin for RNA al. editing)		RNA structure			Stockholm	GPL	link
S2S RNA editor	2D structure	Rnalign	No	base-base interactions,2D,3D viewer	FASTA, RnaML	Free	link
Seaview	No	local Muscle/ClustalW	Parsimony, distance methods, PhyML	Dot-plot, vim-like editing keys	Nexus, MSF, Clustal, FASTA, PHYLIP, MASE		link
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, DragNdrop from external URL from within the user interface	Freeware	link
SeqPop	No					Free	link
Sequlator	No	Pairwise alignment	No	easy alignment editing	MSF	Free	link
SnipViz	No	No	No (but can display them)	Pure Javascript and HTML. Suitable for integration into web sites.	FASTA, newick	Apache 2.0	link publication
Strap	Jnet, NNPREDICT, Coiled coil, 16 different TM-helix	Fifteen different Methods	Neighbor-joining	Dot-plot, Structure-neighbors, 3D-superposition, Blast-search, Mutation/SNP analysis, Sequence features, Biojava-interface	MSF, Stockholm, Clustalw, Nexus, FASTA, PDB, Embl, GenBank, hssp, Pfam	GPL	link
Tablet	No	No	No	High-performance graphical viewer for viewing next generation sequence assemblies and alignments.	ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, and GFF3	Open source, (c)James Hutton Institute	link
UGENE	Yes	MUSCLE, KAlign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith-Waterman algorithm	Yes	many	FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, CLUSTALW, Stockholm, Newick, PDB, MSF, GFF	GPL	link
VISSA sequence/structure viewer	DSSP secondary structure	ClustalX	No	Mapping from sequence to 3D structure	Clustal, FASTA	Free	link
DNApy	No	MUSCLE	No	Editing of GenBank files, plasmid drawing, ABI chromatograms,	FASTA, FASTQ, GenBank	GPL3	link
Alignment Annotator	Yes	By sequence or mixed sequence and structure	Includes Archaeopteryx	Running in modern web browsers of desktop PCs + tablets (iOS, Android, MS-Mobile). Distributed Annotation System and user defined annotations. Scriptable. Export to HTML, Word and Jalview.	Many	GPL	link

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
• List of software for molecular mechanics modeling