List of alignment visualization software

Short description: Wikipedia list article

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

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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 2021  | 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
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  | ?
ClustalX viewer  | No  | ClustalW  | NJ | Alignment quality analysis  | Nexus, MSF, Clustal, FASTA, PHYLIP | Proprietary, freeware for academic use  | No  | Command line
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 noncomercial 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 JNET | Clustal, MUSCLE, MAFFT, Probcons, TCoffee via web services  | UPGMA, NJ | Sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval.  | FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm | Free, GPL | Applet  | Cross-platform -Mac OS, Linux,

Windows

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  | Proprietary, freeware | ?  | ?
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

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