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 LicenseCan run on BrowserOperating Platforms Link Alan Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding FASTA, Clustal , GPL 3NoLinux Terminal Ale (emacs plugin) GenBank, EMBL, FASTA, PHYLIP , GPLNoGNU Emacs AliView 1.31.x (updated Feb 2026) 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 , GPL 3NoCross-platform -Mac OS,

Linux,

Windows alv Console-based (no GUI), yet with colors. Coding DNA is coloured by codon. FASTA, PHYLIP, Nexus, Clustal, Stockholm , GPL 3 NoCross-platform , see also arb 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 , freeware, arb license, open modifiable source NoLinux, Mac OS (homebrew) Base-By-Base Visual summary, percent identity tables, some integrated advanced analysis tools Genbank, FASTA, EMBEL, Clustal, base-by-base files , freeware, must registerNoWindows / macOS / Linux BioEdit Plasmid drawing, ABI chromatograms, Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR , freewareNoWindows (95/98/NT/2000/XP) BioNumerics Genbank, FASTA , commercialNoWindows as a client application bioSyntax Native syntax highlighting support for Vim, less, gedit and Sublime FASTA, FASTQ, Clustal, SAM, VCF and more , GPL 3NoVim, Less, GEdit, & Sublime BoxShade Specifically for multiple alignments MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW , public domainNoMSDOS, VMS CINEMA , but can read-show 2D structure annotations Dotplot, 6 frame translation, Blast Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS , freewareNoCross-platform -Mac OS, Linux, Windows CLC viewer (free version) Workflows, blast-genbank search many , freeware. More options available in commercial versions.NoWindows / macOS / Linux CIAlign Alignment visualisation as publication-ready images, alignment cleaning. FASTA , MIT No Linux, Windows, MacOS Publication ClustalX viewer Alignment quality analysis Nexus, MSF, Clustal, FASTA, PHYLIP , freeware for academic useNoCommand line CodonCode Aligner 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 , commercial, Viewer is FreewareNoMac OS, Windows Cylindrical Alignment App 3D, animation, drilldown, legend selection BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT , CDDL 1. Available for dual licensing.NoCross-platform -Mac OS, Linux, Windows Cylindrical BLAST Viewer 3D, animation, drilldown, legend selection BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT , GPLNoLinux, Windows, MacOS DECIPHER Primer-Probe design, Chimera finding FASTA, FASTQ, GenBank , GPLNoMac OS, Windows Discovery Studio 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, ... , commercial, Viewer is FreewareNoLinux, Windows DnaSP Can compute several population genetics statistics, reconstruct haplotypes with PHASE FASTA, Nexus, MEGA, PHYLIP , commercial, freeware for noncommercial useNoCross-platform -Mac OS, Linux, Windows DNASTAR Lasergene Molecular Biology Suite 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 , commercial, academic licenses availableNoMac OS, Windows emacs - biomode , GPLNo? FLAK Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options FASTA , commercial, freeware for noncommercial useNo? Genedoc , but can read-show annotations , but can read-show annotations gel simulation, stats, multiple views, simple many , freewareNo? table of features Geneious - powered by EMBOSS tools Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more >40 file formats imported and exported , commercial; personal, floatingYesCross-platform - Mac, Windows, Linux Integrated Genome Browser (IGB) Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers BAM, FASTA, PSL , CPLNoCross-platform - Mac, Windows, Linux interactive Tree Of Life (iTOL) 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 , free useYesBrowser IVisTMSA 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 , freewareNo? www.ivistmsa.com Jalview 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. , GPLJalviewJS (JavaScript)Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine. Jevtrace 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 , commercial, freeware for academic useNoCross-platform -Mac OS, Linux,

Windows manual JSAV A JavaScript component allowing integrating an alignment viewer into web pages An array of JavaScript objects , GPL 2YesBrowser Lucid Align Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data BAM, FASTQ, FASTA , commercial, freeware for academic useNoMac OS Maestro Mapping from sequence to 3D structure, structure-sequence editing-modeling Clustal, FASTA PDB , freeware for academic useNo? MEGA Extended support to phylogenetics analysis FASTA, Clustal, Nexus, MEGA, etc. , freeware, must registerNo? Molecular Operating Environment (MOE) 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 No? MSAReveal.org 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 , Creative Commons Attribution NonCommercial Share-alikeYes? Multiseq (VMD plugin) , but can display and align 3D structures Scripting via Tcl, mapping from sequence to 3D structure FASTA, PDB, ALN, PHYLIP, NEXUS , freeware, but VMD is free for noncommercial use onlyNo? MView Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF , GPLNoCross-platform - Mac OS, Linux, Windows PFAAT , but can display 3D structures Manual annotation, conservation scores Nexus, MSF, Clustal, FASTA, PFAAT , freewareNo? Ralee (emacs plugin for RNA al. editing) Stockholm , GPLNo? S2S RNA editor Base-base interactions, 2D-3D viewer FASTA, RnaML , freewareNo? Seaview Dot-plot, vim-like editing keys Nexus, MSF, Clustal, FASTA, PHYLIP, MASE , GPL 3No Linux, Mac OS, Windows SeqTUI sequence translation, supermatrix construction, SNP extraction, terminal-based interactive navigation Nexus, FASTA, PHYLIP , MIT Linux, Mac OS, Windows, terminal Seqotron Manual alignment, tree visualisation Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat , GPLNoMac OS X publication Sequilab 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 , freewareNo? SeqPup , freewareNo? Sequlator easy alignment editing MSF , freewareNo? SnipViz (but can display them) Pure JavaScript and HTML; suitable to integrate in websites FASTA, newick , Apache 2.0YesBrowsers , publication Strap 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 , GPLNo? Tablet High-performance graphical viewer for viewing next generation sequence assemblies and alignments. ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3 , BSD 2-clauseNo? UGENE Many FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFF , GPLNo? VISSA sequence-structure viewer Mapping from sequence to 3D structure Clustal, FASTA , freewareNo? DNApy Editing of GenBank files, plasmid drawing, ABI chromatograms, FASTA, FASTQ, GenBank , GPL 3?? Alignment Annotator DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview. Many , GPLYesiOS, Android, MS-Mobile, Browsers

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