Menu
Home
People
Places
Arts
History
Plants & Animals
Science
Life & Culture
Technology
Reference.org
List of alignment visualization software
open-in-new
<h2 id="alignment-viewers-editors">Alignment viewers, editors</h2> <table><tbody><tr><th>Name</th><th>Structure prediction tools integrated</th><th>Can align sequences</th><th>Can calculate phylogenetic trees</th><th>Other features</th><th>Format support</th><th><a href="/facts/Software_license/7enfIqhL">License</a></th><th>Can run on Browser</th><th>Operating Platforms</th><th>Link</th></tr><tr><td>Alan</td><td>No</td><td>No</td><td>No</td><td>Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>No</td><td>Linux Terminal</td><td><a href="https://github.com/mpdunne/alan">Official website</a></td></tr><tr><td>Ale (<a href="/facts/Emacs/BvGxuAxQ">emacs</a> plugin)</td><td>No</td><td>Yes</td><td>No</td><td>No</td><td>GenBank, EMBL, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>No</td><td>GNU Emacs</td><td><a href="http://www.red-bean.com/ale">Official website</a></td></tr><tr><td>AliView 2025</td><td>No</td><td>MUSCLE integrated; other programs such as MAFFT can be defined</td><td>External programs such as FastTree can be called from within</td><td>Fast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/FASTQ/stcjJR9o">FASTQ</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>?</td><td>Cross-platform -Mac OS,<p>Linux, </p><p>Windows</p></td><td><a href="http://www.ormbunkar.se/aliview">Official website</a></td></tr><tr><td>alv</td><td>No</td><td>No</td><td>No</td><td>Console-based (no GUI), yet with colors. Coding DNA is coloured by codon.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Nexus_file/YvuV615G">Nexus</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>No</td><td>Cross-platform</td><td><a href="https://pypi.org/project/alv/">Official website</a>, see also <a href="https://github.com/arvestad/alv">alv</a> on <a href="/facts/GitHub/n1hNCsc3">GitHub</a></td></tr><tr><td><a href="/facts/ARB_Project/2J8TBFvN">arb</a></td><td>structure editable, show bond in helix sequence regions, 2D molecule viewer</td><td>MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)</td><td>arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayes</td><td>Edits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and <a href="http://www.arb-home.de/images/arb_secedit_large.png">visualizes probes</a>.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/GenBank/XyMcrktE">GenBank</a>, <a href="/facts/EMBL/uPTzUQB8">EMBL</a>, <a href="/facts/Newick_format/CpLFja9e">Newick</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a>, <a href="http://vc.arb-home.de/readonly/trunk/arb_LICENSE.txt">arb license</a>, open modifiable source</td><td>No</td><td>Linux, Mac OS (homebrew)</td><td><a href="http://www.arb-home.de/">Official website</a></td></tr><tr><td>Base-By-Base</td><td>No</td><td>MUSCLE</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, complete and single linkages, WPMGA</td><td>Visual summary, percent identity tables, some integrated advanced analysis tools</td><td>Genbank, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, EMBEL, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, base-by-base files</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a>, must register</td><td>?</td><td>?</td><td><a href="http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base">Official website</a></td></tr><tr><td>BioEdit</td><td>No</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td>Rudimentary, can read <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a></td><td>Plasmid drawing, ABI chromatograms,</td><td>Genbank, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a> 3.2 and 4, NBRF-PIR</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>No</td><td>Windows (95/98/NT/2000/XP)</td><td><a href="http://www.mbio.ncsu.edu/BioEdit/bioedit.html">Official website</a></td></tr><tr><td><a href="/facts/BioNumerics/juh3N9E0">BioNumerics</a></td><td>No</td><td>Yes</td><td>Yes</td><td>?</td><td>Genbank, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a></td><td>?</td><td>?</td><td><a href="http://www.applied-maths.com/bionumerics/bionumerics.htm">Official website</a></td></tr><tr><td>bioSyntax</td><td>No</td><td>No</td><td>No</td><td>Native syntax highlighting support for <a href="/facts/Vim_(text_editor)/JXAYMDgt">Vim</a>, <a href="/facts/Less_(Unix)/dV6K2hne">less</a>, <a href="/facts/Gedit/Eroyyson">gedit</a> and <a href="/facts/Sublime_Text/8GzJSGEr">Sublime</a></td><td><a href="/facts/FASTA/YetQcbUz">FASTA</a>, <a href="/facts/FASTQ/stcjJR9o">FASTQ</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/SAM_(file_format)/0JMSBdGW">SAM</a>, <a href="/facts/Variant_Call_Format/MMlhEPYg">VCF</a> and more</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>No</td><td>Vim, Less, GEdit, & Sublime</td><td><a href="https://bioSyntax.org">Official website</a></td></tr><tr><td>BoxShade</td><td>No</td><td>No</td><td>No</td><td>Specifically for multiple alignments</td><td>MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by <a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td>Free, <a href="/facts/Public_domain/YWKMDKw4">public domain</a></td><td>No</td><td>MSDOS, VMS</td><td><a href="http://ch.embnet.org/software/BOX_form.html">Official website</a></td></tr><tr><td>CINEMA</td><td>No, but can read-show 2D structure annotations</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td>No</td><td>Dotplot, 6 frame translation, Blast</td><td><a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, PRINTS</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>No</td><td>Cross-platform -Mac OS, Linux, Windows</td><td><a href="http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php">Official website</a></td></tr><tr><td>CLC viewer (free version)</td><td>Commercial version only</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>, MUSCLE, T-Coffee, MAFFT, Kalign, various</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a></td><td>Workflows, blast-genbank search</td><td>many</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a>. More options available in commercial versions.</td><td>No</td><td>?</td><td><a href="http://www.clcbio.com">Official website</a></td></tr><tr><td>CIAlign</td><td>No</td><td>No</td><td>No</td><td>Alignment visualisation as publication-ready images, alignment cleaning.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a></td><td>Free, <a href="/facts/MIT_License/8llAQtlk">MIT</a></td><td>No</td><td>Linux, Windows, MacOS</td><td><a href="https://github.com/KatyBrown/CIAlign">Official website</a><p>Publication</p></td></tr><tr><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>X viewer</td><td>No</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td><a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a></td><td>Alignment quality analysis</td><td><a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for academic use</td><td>No</td><td>Command line</td><td><a href="http://www.clustal.org">Official website</a></td></tr><tr><td>Cylindrical Alignment App</td><td>No</td><td>No</td><td>No</td><td>3D, animation, drilldown, legend selection</td><td>BLAST XML, proprietary XML, GFF3, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, INSDSet, user expandable with <a href="/facts/XSLT/0gw4WVyJ">XSLT</a></td><td>Free, <a href="/facts/Common_Development_and_Distribution_License/f1gcKWVz">CDDL 1.</a> Available for dual licensing.</td><td>?</td><td>Cross-platform -Mac OS, Linux, Windows</td><td><a href="http://sourceforge.net/projects/cylindrical-alignment-app">Official website</a></td></tr><tr><td>Cylindrical BLAST Viewer</td><td>No</td><td>No</td><td>No</td><td>3D, animation, drilldown, legend selection</td><td>BLAST XML, proprietary XML, GFF3, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, INSDSet, user expandable with <a href="/facts/XSLT/0gw4WVyJ">XSLT</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>?</td><td><a href="http://sourceforge.net/projects/cyl-viewer">Official website</a></td></tr><tr><td>DECIPHER</td><td>Yes</td><td>Yes</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, ML</td><td>Primer-Probe design, Chimera finding</td><td>FASTA, FASTQ, GenBank</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>No</td><td>Mac OS, Windows</td><td><a href="http://decipher.cee.wisc.edu/Download.html">Official website</a></td></tr><tr><td>Discovery Studio</td><td>Yes</td><td>Align123, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, S-ALIGN</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, with bootstrap and best tree</td><td>Visualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, more</td><td>BSML, EMBL, GB, HELM, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA/YetQcbUz">FASTA</a>, GDE, <a href="/facts/Protein_Data_Bank_(file_format)/NEMP1sAX">PDB</a>, SEQ, SPT, ...</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, Viewer is <a href="/facts/Freeware/c8oGA9ju">Freeware</a></td><td>?</td><td>Linux, Windows</td><td><a href="http://accelrys.com/products/discovery-studio/visualization-download.php">Official website</a></td></tr><tr><td>DnaSP</td><td>?</td><td>?</td><td>?</td><td>Can compute several population genetics statistics, reconstruct haplotypes with PHASE</td><td><a href="/facts/FASTA/YetQcbUz">FASTA</a>, <a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MEGA, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for noncommercial use</td><td>?</td><td>Cross-platform -Mac OS, Linux, Windows</td><td><a href="http://www.ub.es/dnasp">Official website</a></td></tr><tr><td>DNASTAR Lasergene Molecular Biology Suite</td><td>Yes</td><td>Yes</td><td>Yes</td><td>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</td><td>ABI, DNA Multi-Seq, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, GCG Pileup, GenBank, Phred</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, academic licenses available</td><td>?</td><td>Mac OS, Windows</td><td><a href="http://www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx">Official website</a></td></tr><tr><td><a href="/facts/Emacs/BvGxuAxQ">emacs</a> - biomode</td><td>?</td><td>?</td><td>?</td><td>?</td><td>?</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>?</td><td><a href="http://archive.debian.net/lenny/biomode">Official website</a></td></tr><tr><td>FLAK</td><td>No</td><td>Can perform fuzzy whole genome alignment</td><td>No</td><td>Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options</td><td>FASTA</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for noncommercial use</td><td>?</td><td>?</td><td><a href="http://flakbio.com">Official website</a></td></tr><tr><td>Genedoc</td><td>No, but can read-show annotations</td><td>Pairwise</td><td>No, but can read-show annotations</td><td>gel simulation, stats, multiple views, simple</td><td>many</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://www.nrbsc.org/gfx/genedoc">Official website</a> <a href="http://www.nrbsc.org/gfx/genedoc/gdpaf.htm">table of features</a></td></tr><tr><td>Geneious</td><td>Yes - powered by <a href="/facts/EMBOSS/91ddC2or">EMBOSS</a> tools</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>, MUSCLE, MAUVE, profile, translation</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, PhyML, MrBayes plugin, PAUP* plugin</td><td>Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more</td><td>>40 file formats imported and exported</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>; personal, floating</td><td>?</td><td>Cross-platform - Mac, Windows, Linux</td><td><a href="http://www.geneious.com">Official website</a></td></tr><tr><td><a href="/facts/Integrated_Genome_Browser/g5cKB7dp">Integrated Genome Browser</a> (IGB)</td><td>No</td><td>No</td><td>No</td><td>Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers</td><td>BAM, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, PSL</td><td>Free, <a href="/facts/Common_Public_License/M12x3DgF">CPL</a></td><td>?</td><td>Cross-platform - Mac, Windows, Linux</td><td><a href="http://igb.bioviz.org">Official website</a></td></tr><tr><td>interactive Tree Of Life (iTOL)</td><td>No</td><td>No</td><td>?</td><td>Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments.</td><td>FASTA</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, free use</td><td>Yes</td><td>Browser</td><td><a href="http://itol.embl.de">Official website</a></td></tr><tr><td>IVisTMSA</td><td>No</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a> Omega, ClustalW2, MAFFT, MUSCLE, <a href="/facts/BioJava/337yp2fF">BioJava</a> are integrated to construct alignment</td><td>Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using <a href="/facts/Archaeopteryx_(evolutionary_tree_visualization_and_analysis)/U31U8ms8">Archaeopteryx</a></td><td>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, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a> generator and MSA ID matrix calculator</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W, MSF, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, GDE, Nexus</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td>www.ivistmsa.com</td></tr><tr><td><a href="/facts/Jalview/0bPrdWPx">Jalview</a></td><td>Secondary structure prediction via <a href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred 4</a></td><td><a href="/facts/Clustal/qloHgBMf">Clustal O</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, GLprobs, MSAprobs, <a href="/facts/MUSCLE_(alignment_software)/Qw9GWV6m">MUSCLE</a>, <a href="/facts/MAFFT/stcAIeTJ">MAFFT</a>, Probcons, TCoffee, via web services</td><td><a href="/facts/UPGMA/XbJ1rIrl">UPGMA</a>, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a></td><td>Sequences and features retrieved from user-configurable and publicly registered servers, e.g. <a href="/facts/European_Molecular_Biology_Laboratory/uPTzUQB8">EMBL</a>, <a href="/facts/European_Bioinformatics_Institute/g1GsqPXd">EBI</a>, <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a>, <a href="/facts/Pfam/BKJa293w">Pfam</a>, <a href="/facts/Rfam/pl9awpRM">Rfam</a>, <a href="/facts/UniProt/lfDDHjAl">UniProt</a> Accession retrieval. Structure/model data retrieval from <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a> and 3D-Beacons including <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDBe</a>, <a href="/facts/AlphaFold/DwBhppKC">AlphaFold DB</a>, <a href="/facts/Swiss-model/M9bFT2L9">SWISS-MODEL</a>.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/Pfam/BKJa293w">Pfam</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, BLC, <a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, <a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a>, <a href="/facts/Variant_Call_Format/MMlhEPYg">VCF</a>, AMSA, BioJSON, Clustal, <a href="/facts/European_Nucleotide_Archive/Fsjx6X24">ENA</a>, <a href="/facts/GenBank/XyMcrktE">GenBank</a>, <a href="/facts/General_feature_format/Lh8lDVe4">GFF2</a>, <a href="/facts/General_feature_format/Lh8lDVe4">GFF3</a>, JnetFile, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Pileup_format/uXYyNWas">PileUp</a>, RNAML, <a href="/facts/Crystallographic_Information_File/K1BmBU3h">CIF</a>, <a href="/facts/Crystallographic_Information_File/K1BmBU3h">mmCIF</a>, <a href="/facts/Protein_Data_Bank_(file_format)/NEMP1sAX">PDB</a>.</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td><a href="https://www.jalview.org/jalview-js/">JalviewJS</a> (Javascript)</td><td>Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine.</td><td><a href="https://www.jalview.org/">Official website</a></td></tr><tr><td>Jevtrace</td><td>Integrated with structure viewer <a href="http://www.cmpharm.ucsf.edu/~walther/webmol.html">WebMol</a></td><td>No</td><td>No</td><td>A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive <a href="https://www.ncbi.nlm.nih.gov/pubmed/8609628">Evolutionary Trace</a> and other phylogeny inspired analysis.</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Newick_format/CpLFja9e">Newick</a>, <a href="/facts/Protein_Data_Bank_(file_format)/NEMP1sAX">PDB</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for academic use</td><td>?</td><td>Cross-platform -Mac OS, Linux,<p>Windows</p></td><td><a href="http://compbio.berkeley.edu/people/marcin/jevtrace">Official website</a> <a href="http://compbio.berkeley.edu/people/marcin/jevtrace/jevtracev3.12_manual.pdf">manual</a></td></tr><tr><td>JSAV</td><td>No</td><td>No</td><td>No</td><td>A JavaScript component allowing integrating an alignment viewer into web pages</td><td>An array of JavaScript objects</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 2</td><td>Yes</td><td>Browser</td><td><a href="http://www.bioinf.org.uk/software/jsav">Official website</a></td></tr><tr><td>Lucid Align</td><td>No</td><td>No</td><td>No</td><td>Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data</td><td>BAM, FASTQ, FASTA</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Commercial_software/WLgyRFMh">commercial</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for academic use</td><td>No</td><td>Mac OS</td><td><a href="https://www.lucidalign.com">Official website</a></td></tr><tr><td>Maestro</td><td>Yes</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>X</td><td>Yes</td><td>Mapping from sequence to 3D structure, structure-sequence editing-modeling</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a> <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a> for academic use</td><td>?</td><td>?</td><td><a href="http://www.schrodinger.com/products/14/12">Official website</a></td></tr><tr><td><a href="/facts/MEGA%2c_Molecular_Evolutionary_Genetics_Analysis/jcP1k8tU">MEGA</a></td><td>No</td><td>Native <a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td>UPGMA, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, ME, MP, with bootstrap and confidence test</td><td>Extended support to phylogenetics analysis</td><td>FASTA, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, Nexus, MEGA, etc.</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a>, must register</td><td>?</td><td>?</td><td><a href="http://www.megasoftware.net">Official website</a></td></tr><tr><td><a href="/facts/Molecular_Operating_Environment/YmhIJ3dS">Molecular Operating Environment</a> (MOE)</td><td>Yes</td><td>Yes</td><td>Yes</td><td>Part of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc.</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a>, EMBL, GCG, GCG_MSF, Genbank, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, raw_seq</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a></td><td>?</td><td>?</td><td><a href="http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm">Official website</a></td></tr><tr><td>MSAReveal.org</td><td>No</td><td>No</td><td>No</td><td>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.</td><td>FASTA</td><td>Free, <a href="/facts/Creative_Commons_license/6AV3V7UJ">Creative Commons</a> Attribution NonCommercial <a href="/facts/Share-alike/lKVrDBNE">Share-alike</a></td><td>?</td><td>?</td><td><a href="http://msareveal.org">Official website</a></td></tr><tr><td>Multiseq (<a href="/facts/Visual_Molecular_Dynamics/J53Mox6h">VMD</a> plugin)</td><td>No, but can display and align 3D structures</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W, MAFFT, Stamp (Structural)</td><td>Percent identity, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, MAFFT, Structural</td><td>Scripting via <a href="/facts/Tcl/s7fbKYtR">Tcl</a>, mapping from sequence to 3D structure</td><td>FASTA, PDB, ALN, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, NEXUS</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a>, but VMD is free for noncommercial use only</td><td>?</td><td>?</td><td><a href="http://www.scs.illinois.edu/schulten/multiseq">Official website</a></td></tr><tr><td>MView</td><td>No</td><td>No</td><td>No</td><td>Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns</td><td>BLAST search, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a> search, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, HSSP, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, MSF</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>No</td><td>Cross-platform - Mac OS, Linux, Windows</td><td><a href="http://desmid.github.io/mview">Official website</a></td></tr><tr><td>PFAAT</td><td>No, but can display 3D structures</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td><a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a></td><td>Manual annotation, conservation scores</td><td><a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, PFAAT</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://pfaat.sourceforge.net">Official website</a></td></tr><tr><td>Ralee (emacs plugin for RNA al. editing)</td><td>?</td><td>RNA structure</td><td>?</td><td>?</td><td><a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>?</td><td><a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257">Official website</a></td></tr><tr><td>S2S RNA editor</td><td>2D structure</td><td>Rnalign</td><td>No</td><td>Base-base interactions, 2D-3D viewer</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, RnaML</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://bioinformatics.org/S2S">Official website</a></td></tr><tr><td>Seaview</td><td>No</td><td>local MUSCLE-<a href="/facts/Clustal/qloHgBMf">Clustal</a>W</td><td>Parsimony, distance methods, PhyML</td><td>Dot-plot, <a href="/facts/Vim_(text_editor)/JXAYMDgt">vim</a>-like editing keys</td><td><a href="/facts/Nexus_file/YvuV615G">Nexus</a>, MSF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, MASE</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>?</td><td>Linux, Mac OS, Windows</td><td><a href="http://pbil.univ-lyon1.fr/software/seaview.html">Official website</a></td></tr><tr><td>Seqotron</td><td>No</td><td><a href="/facts/MUSCLE_(alignment_software)/Qw9GWV6m">MUSCLE</a>, <a href="/facts/MAFFT/stcAIeTJ">MAFFT</a></td><td><a href="/facts/UPGMA/XbJ1rIrl">UPGMA</a>, <a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a>, ML (Physher)</td><td>Manual alignment, tree visualisation</td><td><a href="/facts/Nexus_file/YvuV615G">Nexus</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/PHYLIP/Ga4klSvu">PHYLIP</a>, <a href="/facts/MEGA%2c_Molecular_Evolutionary_Genetics_Analysis/jcP1k8tU">MEGA</a>, <a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a>, NBRF/<a href="/facts/Protein_Information_Resource/wHD5WbCB">PIR</a>, GDE flat</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>Mac OS X</td><td><a href="https://github.com/4ment/seqotron">Official website</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/26887850">publication</a></td></tr><tr><td>Sequilab</td><td>Yes</td><td>Yes</td><td>No</td><td>Link alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbars</td><td>Accession number, GI number, PDB ID, <a href="/facts/FASTA/YetQcbUz">FASTA</a>, drag-drop from external <a href="/facts/URL/pPD5g7Wq">URL</a> from within the user interface</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://www.sequilab.org">Official website</a></td></tr><tr><td>SeqPup</td><td>No</td><td>?</td><td>?</td><td>?</td><td>?</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://iubioarchive.bio.net/soft/molbio/seqpup/java/">Official website</a></td></tr><tr><td>Sequlator</td><td>No</td><td>Pairwise alignment</td><td>No</td><td>easy alignment editing</td><td>MSF</td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://sequlator.com">Official website</a></td></tr><tr><td>SnipViz</td><td>No</td><td>No</td><td>No (but can display them)</td><td>Pure Javascript and HTML; suitable to integrate in websites</td><td>FASTA, newick</td><td>Free, <a href="/facts/Apache_License/5AeIjas8">Apache</a> 2.0</td><td>Yes</td><td>Browsers</td><td><a href="https://github.com/yeastrc/snipviz">Official website</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/25056180/">publication</a></td></tr><tr><td>Strap</td><td>Jnet, NNPREDICT, Coiled coil, 16 different TM-helix</td><td>15 different methods</td><td><a href="/facts/Neighbor_joining/Yld9VDz5">NJ</a></td><td>Dot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, <a href="/facts/BioJava/337yp2fF">BioJava</a>-interface</td><td>MSF, <a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a>, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, <a href="/facts/Nexus_file/YvuV615G">Nexus</a>, <a href="/facts/FASTA/YetQcbUz">FASTA</a>, <a href="/facts/Protein_Data_Bank_(file_format)/NEMP1sAX">PDB</a>, Embl, <a href="/facts/GenBank/XyMcrktE">GenBank</a>, hssp, <a href="/facts/Pfam/BKJa293w">Pfam</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>?</td><td><a href="http://3d-alignment.eu">Official website</a></td></tr><tr><td>Tablet</td><td>No</td><td>No</td><td>No</td><td>High-performance graphical viewer for viewing next generation sequence assemblies and alignments.</td><td><a href="/facts/ACE_(genomic_file_format)/tY5Lbcjq">ACE</a>, AFG, MAQ, SOAP2, <a href="/facts/BAM_format/WFzNmNVs">SAM</a>, <a href="/facts/BAM_format/WFzNmNVs">BAM</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/FASTQ_format/stcjJR9o">FASTQ</a>, <a href="/facts/General_feature_format/Lh8lDVe4">GFF3</a></td><td>Free, <a href="/facts/BSD_licenses/XLtmLp5x">BSD</a> 2-clause</td><td>?</td><td>?</td><td><a href="http://ics.hutton.ac.uk/tablet">Official website</a></td></tr><tr><td><a href="/facts/UGENE/mjzAH719">UGENE</a></td><td>Yes</td><td><a href="/facts/MUSCLE_(alignment_software)/Qw9GWV6m">MUSCLE</a>, Kalign, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, ClustalO, ClustalX, <a href="/facts/MAFFT/stcAIeTJ">MAFFT</a>, <a href="/facts/T-Coffee/kS458MqX">T-Coffee</a>, <a href="/facts/Smith%25E2%2580%2593Waterman_algorithm/pvfmhpQB">Smith–Waterman algorithm</a></td><td>Yes</td><td>Many</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/FASTQ_format/stcjJR9o">FASTQ</a>, <a href="/facts/GenBank/XyMcrktE">GenBank</a>, <a href="/facts/EMBL/uPTzUQB8">EMBL</a>, ABIF, SCF, <a href="/facts/Clustal/qloHgBMf">Clustal</a>W, <a href="/facts/Stockholm_format/VGLJXwqr">Stockholm</a>, Newick, <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a>, MSF, GFF</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>?</td><td>?</td><td><a href="http://ugene.unipro.ru">Official website</a></td></tr><tr><td>VISSA sequence-structure viewer</td><td>DSSP secondary structure</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>X</td><td>No</td><td>Mapping from sequence to 3D structure</td><td><a href="/facts/Clustal/qloHgBMf">Clustal</a>, <a href="/facts/FASTA_format/uPfYMPam">FASTA</a></td><td><a href="/facts/Proprietary_software/9zcskxYL">Proprietary</a>, <a href="/facts/Freeware/c8oGA9ju">freeware</a></td><td>?</td><td>?</td><td><a href="http://bioinformatics.burnham.org/liwz/vissa">Official website</a></td></tr><tr><td>DNApy</td><td>No</td><td><a href="/facts/MUSCLE_(alignment_software)/Qw9GWV6m">MUSCLE</a></td><td>No</td><td>Editing of GenBank files, plasmid drawing, ABI chromatograms,</td><td><a href="/facts/FASTA_format/uPfYMPam">FASTA</a>, <a href="/facts/FASTQ_format/stcjJR9o">FASTQ</a>, <a href="/facts/GenBank/XyMcrktE">GenBank</a></td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a> 3</td><td>?</td><td>?</td><td><a href="https://github.com/mengqvist/DNApy">Official website</a></td></tr><tr><td>Alignment Annotator</td><td>Yes</td><td>By sequence or mixed sequence and structure</td><td>Includes <a href="/facts/Archaeopteryx_(evolutionary_tree_visualization_and_analysis)/U31U8ms8">Archaeopteryx</a></td><td>DAS and user defined annotations. Scriptable. Export to HTML, Word, <a href="/facts/Jalview/0bPrdWPx">Jalview</a>.</td><td>Many</td><td>Free, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL</a></td><td>Yes</td><td>iOS, Android, MS-Mobile,<p>Browsers</p></td><td><a href="http://www.bioinformatics.org/strap/aa">Official website</a></td></tr></tbody></table> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Sequence_alignment_software/6AJKAI0p">Sequence alignment software</a></li> <li><a href="/facts/Biological_data_visualization/XISBFDuf">Biological data visualization</a></li> <li><a href="/facts/Comparison_of_software_for_molecular_mechanics_modeling/RabeF7vR">Comparison of software for molecular mechanics modeling</a></li></ul>