List of alignment visualization software

Template:Short description This page is a subsection of the list of sequence alignment software.

Multiple alignment visualization tools typically serve four purposes:

• 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.

Alignment viewers, editors

Name	Structure prediction tools integrated	Can align sequences	Can calculate phylogenetic trees	Other features	Format support	License	Can run on Browser	Operating Platforms	Link
Alan	No	No	No	Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding	FASTA, Clustal	Free, GPL 3	No	Linux Terminal
Ale (emacs plugin)	No	Yes	No	No	GenBank, EMBL, FASTA, PHYLIP	Free, GPL	No	GNU Emacs
AliView 2025	No	MUSCLE integrated; other programs such as MAFFT can be defined	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, FASTQ, PHYLIP, Nexus, MSF, Clustal	Free, GPL 3	?	Cross-platform -Mac OS, Linux, Windows
alv	No	No	No	Console-based (no GUI), yet with colors. Coding DNA is coloured by codon.	FASTA, PHYLIP, Nexus, Clustal, Stockholm	Free, GPL 3	No	Cross-platform	, see also Template:GitHub
arb	structure editable, show bond in helix sequence regions, 2D molecule viewer	MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)	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 visualizes probes.	FASTA, GenBank, EMBL, Newick	Proprietary, freeware, arb license, open modifiable source	No	Linux, Mac OS (homebrew)
Base-By-Base	No	MUSCLE	UPGMA, NJ, complete and single linkages, WPMGA	Visual summary, percent identity tables, some integrated advanced analysis tools	Genbank, FASTA, EMBEL, Clustal, base-by-base files	Proprietary, freeware, must register	?	?
BioEdit	No	ClustalW	Rudimentary, can read PHYLIP	Plasmid drawing, ABI chromatograms,	Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR	Proprietary, freeware	No	Windows (95/98/NT/2000/XP)
BioNumerics	No	Yes	Yes	?	Genbank, FASTA	Proprietary, commercial	?	?
bioSyntax	No	No	No	Native syntax highlighting support for Vim, less, gedit and Sublime	FASTA, FASTQ, Clustal, SAM, VCF and more	Free, GPL 3	No	Vim, Less, GEdit, & Sublime
BoxShade	No	No	No	Specifically for multiple alignments	MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW	Free, public domain	No	MSDOS, VMS
CINEMA	No, but can read-show 2D structure annotations	ClustalW	No	Dotplot, 6 frame translation, Blast	Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS	Proprietary, freeware	No	Cross-platform -Mac OS, Linux, Windows
CLC viewer (free version)	Commercial version only	Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various	UPGMA, NJ	Workflows, blast-genbank search	many	Proprietary, freeware. More options available in commercial versions.	No	?
CIAlign	No	No	No	Alignment visualisation as publication-ready images, alignment cleaning.	FASTA	Free, MIT	No	Linux, Windows, MacOS	Publication
ClustalX viewer	No	ClustalW	NJ	Alignment quality analysis	Nexus, MSF, Clustal, FASTA, PHYLIP	Proprietary, freeware for academic use	No	Command line
CodonCode Aligner	no, but can read, add & show structure annotations	Clustal, MUSCLE, various built-in algorithms	Yes	Multi- and pairwise alignments, assembly, sequence translation, editing, trimming, mutation detection, restriction analysis, cloning, primer design, dotplot, much more	ABI, SCF, FASTA, FASTQ, Nexus/PAUP or PHYLIP, Sam, Bam, .dna, EMBL, GenBank, BLAST, GFF	Proprietary, commercial, Viewer is Freeware	No	Mac OS, Windows
Cylindrical Alignment App	No	No	No	3D, animation, drilldown, legend selection	BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT	Free, CDDL 1. Available for dual licensing.	?	Cross-platform -Mac OS, Linux, Windows
Cylindrical BLAST Viewer	No	No	No	3D, animation, drilldown, legend selection	BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT	Free, GPL	?	?
DECIPHER	Yes	Yes	UPGMA, NJ, ML	Primer-Probe design, Chimera finding	FASTA, FASTQ, GenBank	Free, GPL	No	Mac OS, Windows
Discovery Studio	Yes	Align123, ClustalW, S-ALIGN	UPGMA, 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, PDB, SEQ, SPT, ...	Proprietary, commercial, Viewer is Freeware	?	Linux, Windows
DnaSP	?	?	?	Can compute several population genetics statistics, reconstruct haplotypes with PHASE	FASTA, Nexus, MEGA, PHYLIP	Proprietary, commercial, freeware for noncommercial use	?	Cross-platform -Mac OS, Linux, Windows
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, GCG Pileup, GenBank, Phred	Proprietary, commercial, academic licenses available	?	Mac OS, Windows
emacs - biomode	?	?	?	?	?	Free, GPL	?	?
FLAK	No	Can perform fuzzy whole genome alignment	No	Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options	FASTA	Proprietary, commercial, freeware for noncommercial use	?	?
Genedoc	No, but can read-show annotations	Pairwise	No, but can read-show annotations	gel simulation, stats, multiple views, simple	many	Proprietary, freeware	?	?	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, much more	>40 file formats imported and exported	Proprietary, commercial; personal, floating	?	Cross-platform - Mac, Windows, Linux
Integrated Genome Browser (IGB)	No	No	No	Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers	BAM, FASTA, PSL	Free, CPL	?	Cross-platform - Mac, Windows, Linux
interactive Tree Of Life (iTOL)	No	No	?	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
IVisTMSA	No	Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment	Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using 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 generator and MSA ID matrix calculator	ClustalW, MSF, PHYLIP, PIR, GDE, Nexus	Proprietary, freeware	?	?	www.ivistmsa.com
Jalview	Secondary structure prediction via JPred 4	Clustal O, Clustal, GLprobs, MSAprobs, MUSCLE, MAFFT, Probcons, TCoffee, via web services	UPGMA, NJ	Sequences and features retrieved from user-configurable and publicly registered servers, e.g. EMBL, EBI, PDB, Pfam, Rfam, UniProt Accession retrieval. Structure/model data retrieval from PDB and 3D-Beacons including PDBe, AlphaFold DB, SWISS-MODEL.	FASTA, Pfam, MSF, Clustal, BLC, PIR, Stockholm, VCF, AMSA, BioJSON, Clustal, ENA, GenBank, GFF2, GFF3, JnetFile, PHYLIP, PileUp, RNAML, CIF, mmCIF, PDB.	Free, GPL	JalviewJS (Javascript)	Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine.
Jevtrace	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	Proprietary, commercial, freeware for academic use	?	Cross-platform -Mac OS, Linux, Windows	manual
JSAV	No	No	No	A JavaScript component allowing integrating an alignment viewer into web pages	An array of JavaScript objects	Free, GPL 2	Yes	Browser
Lucid Align	No	No	No	Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data	BAM, FASTQ, FASTA	Proprietary, commercial, freeware for academic use	No	Mac OS
Maestro	Yes	ClustalX	Yes	Mapping from sequence to 3D structure, structure-sequence editing-modeling	Clustal, FASTA PDB	Proprietary, freeware for academic use	?	?
MEGA	No	Native ClustalW	UPGMA, NJ, ME, MP, with bootstrap and confidence test	Extended support to phylogenetics analysis	FASTA, Clustal, Nexus, MEGA, etc.	Proprietary, freeware, must register	?	?
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, PDB, EMBL, GCG, GCG_MSF, Genbank, PHYLIP, PIR, raw_seq	Proprietary	?	?
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 Attribution NonCommercial Share-alike	?	?
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, PHYLIP, NEXUS	Proprietary, freeware, but VMD is free for noncommercial use only	?	?
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	Free, GPL	No	Cross-platform - Mac OS, Linux, Windows
PFAAT	No, but can display 3D structures	ClustalW	NJ	Manual annotation, conservation scores	Nexus, MSF, Clustal, FASTA, PFAAT	Proprietary, freeware	?	?
Ralee (emacs plugin for RNA al. editing)	?	RNA structure	?	?	Stockholm	Free, GPL	?	?
S2S RNA editor	2D structure	Rnalign	No	Base-base interactions, 2D-3D viewer	FASTA, RnaML	Proprietary, freeware	?	?
Seaview	No	local MUSCLE-ClustalW	Parsimony, distance methods, PhyML	Dot-plot, vim-like editing keys	Nexus, MSF, Clustal, FASTA, PHYLIP, MASE	Free, GPL 3	?	Linux, Mac OS, Windows
Seqotron	No	MUSCLE, MAFFT	UPGMA, NJ, ML (Physher)	Manual alignment, tree visualisation	Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat	Free, GPL	?	Mac OS X	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	?	?
SeqPup	No	?	?	?	?	Proprietary, freeware	?	?
Sequlator	No	Pairwise alignment	No	easy alignment editing	MSF	Proprietary, freeware	?	?
SnipViz	No	No	No (but can display them)	Pure Javascript and HTML; suitable to integrate in websites	FASTA, newick	Free, Apache 2.0	Yes	Browsers	, publication
Strap	Jnet, NNPREDICT, Coiled coil, 16 different TM-helix	15 different methods	NJ	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	Free, GPL	?	?
Tablet	No	No	No	High-performance graphical viewer for viewing next generation sequence assemblies and alignments.	ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3	Free, BSD 2-clause	?	?
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	Free, GPL	?	?
VISSA sequence-structure viewer	DSSP secondary structure	ClustalX	No	Mapping from sequence to 3D structure	Clustal, FASTA	Proprietary, freeware	?	?
DNApy	No	MUSCLE	No	Editing of GenBank files, plasmid drawing, ABI chromatograms,	FASTA, FASTQ, GenBank	Free, GPL 3	?	?
Alignment Annotator	Yes	By sequence or mixed sequence and structure	Includes Archaeopteryx	DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview.	Many	Free, GPL	Yes	iOS, Android, MS-Mobile, Browsers

See also

• Sequence alignment software
• Biological data visualization
• Comparison of software for molecular mechanics modeling