This page is a subsection of the list of sequence alignment software.
Multiple alignment visualization tools typically serve four purposes:
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.
| 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 | Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding | FASTA, Clustal | , GPL 3 | No | Linux Terminal | ||||||
| Ale (emacs plugin) | GenBank, EMBL, FASTA, PHYLIP | , GPL | No | GNU Emacs | |||||||
| AliView 2021 | 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 3 | ? | Cross-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 | No | Cross-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 | No | Linux, 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 register | ? | ? | ||||||
| BioEdit | Plasmid drawing, ABI chromatograms, | Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR | , freeware | No | Windows (95/98/NT/2000/XP) | ||||||
| BioNumerics | Genbank, FASTA | , commercial | ? | ? | |||||||
| bioSyntax | Native syntax highlighting support for Vim, less, gedit and Sublime | FASTA, FASTQ, Clustal, SAM, VCF and more | , GPL 3 | No | Vim, 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 domain | No | MSDOS, VMS | ||||||
| CINEMA | , but can read-show 2D structure annotations | Dotplot, 6 frame translation, Blast | Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS | , freeware | No | Cross-platform -Mac OS, Linux, Windows | |||||
| CLC viewer (free version) | Workflows, blast-genbank search | many | , freeware. More options available in commercial versions. | No | ? | ||||||
| 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 use | No | Command line | ||||||
| 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. | ? | Cross-platform -Mac OS, Linux, Windows | ||||||
| Cylindrical BLAST Viewer | 3D, animation, drilldown, legend selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | , GPL | ? | ? | ||||||
| DECIPHER | Primer-Probe design, Chimera finding | FASTA, FASTQ, GenBank | , GPL | No | Mac 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 Freeware | ? | Linux, Windows | ||||||
| DnaSP | Can compute several population genetics statistics, reconstruct haplotypes with PHASE | FASTA, Nexus, MEGA, PHYLIP | , commercial, freeware for noncommercial use | ? | Cross-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 available | ? | Mac OS, Windows | ||||||
| emacs - biomode | , GPL | ? | ? | ||||||||
| FLAK | Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options | FASTA | , commercial, freeware for noncommercial use | ? | ? | ||||||
| Genedoc | , but can read-show annotations | , but can read-show annotations | gel simulation, stats, multiple views, simple | many | , freeware | ? | ? | 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, floating | ? | Cross-platform - Mac, Windows, Linux | |||||
| Integrated Genome Browser (IGB) | Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers | BAM, FASTA, PSL | , CPL | ? | Cross-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 use | Yes | Browser | ||||||
| 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 | , freeware | ? | ? | 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. | , GPL | JalviewJS (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 use | ? | Cross-platform -Mac OS, Linux, Windows | manual | |||||
| JSAV | A JavaScript component allowing integrating an alignment viewer into web pages | An array of JavaScript objects | , GPL 2 | Yes | Browser | ||||||
| Lucid Align | Lucid Align | BAM, FASTQ, FASTA | Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data | BAM, FASTQ, FASTA | , commercial, freeware for academic use | No | Mac OS | ||||
| Maestro | Mapping from sequence to 3D structure, structure-sequence editing-modeling | Clustal, FASTA PDB | , freeware for academic use | ? | ? | ||||||
| MEGA | Extended support to phylogenetics analysis | FASTA, Clustal, Nexus, MEGA, etc. | , freeware, must register | ? | ? | ||||||
| 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 | ? | ? | |||||||
| 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-alike | ? | ? | ||||||
| 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 only | ? | ? | |||||
| 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 | , GPL | No | Cross-platform - Mac OS, Linux, Windows | ||||||
| PFAAT | , but can display 3D structures | Manual annotation, conservation scores | Nexus, MSF, Clustal, FASTA, PFAAT | , freeware | ? | ? | |||||
| Ralee (emacs plugin for RNA al. editing) | Stockholm | , GPL | ? | ? | |||||||
| S2S RNA editor | Base-base interactions, 2D-3D viewer | FASTA, RnaML | , freeware | ? | ? | ||||||
| Seaview | Dot-plot, vim-like editing keys | Nexus, MSF, Clustal, FASTA, PHYLIP, MASE | , GPL 3 | ? | Linux, Mac OS, Windows | ||||||
| Seqotron | Manual alignment, tree visualisation | Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat | , GPL | ? | Mac 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 | , freeware | ? | ? | ||||||
| SeqPup | , freeware | ? | ? | ||||||||
| Sequlator | easy alignment editing | MSF | , freeware | ? | ? | ||||||
| SnipViz | (but can display them) | Pure Javascript and HTML; suitable to integrate in websites | FASTA, newick | , Apache 2.0 | Yes | Browsers | , 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 | , GPL | ? | ? | ||||||
| Tablet | High-performance graphical viewer for viewing next generation sequence assemblies and alignments. | ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3 | , BSD 2-clause | ? | ? | ||||||
| UGENE | Many | FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFF | , GPL | ? | ? | ||||||
| VISSA sequence-structure viewer | Mapping from sequence to 3D structure | Clustal, FASTA | , freeware | ? | ? | ||||||
| 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 | , GPL | Yes | iOS, Android, MS-Mobile, Browsers |
