Interactive example of overlapping residue annotations. The first sequence has two residue selections indicated by cyan and red background. The second sequence exhibits two residue selections which are shown as red and green underlining. The text information pops up when the mouse is moved.

Multiple Sequence Alignments in HTML
without Java
Web-interface and API

Create alignment documents with the
Web interface


Visualization of richly decorated interactive multiple sequence alignments. Third party software can use Alignment-to-html for alignment computation and visualization. The HTML alignment files can be viewed in all browsers and on all platforms including Android and iOS and does not require plugins and is independent of Java. Client side Java is only required for optional 3D-visualization, 3D-superposition, Jalview and for phylogenetic trees. The client program logic resides in a JavaScript-library file and the data is contained in the generated HTML file. Meta data like protein name, organism, PDB residue number, PDB insertion code, chain letter, coding triplet, exon number and annotations is obtained from files in PDB, Swissprot, Embl, Genbank, Nexus and Stockholm format and displayed while the mouse is moved. Residues can be annotatated directly by commands or by remote BioDAS servers. Send Requests to
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Supported platforms: Google-chrome (recommended), Opera, Firefox, Iceweasel, Safari, IE, Epiphany, Konquerer, Android, iOS.
Citation: Christoph Gille, Weyand Birgit and Andreas Gille: Sequence alignment visualization in HTML5 without Java (2013) Bioinformatics (30), 121-122 Full text Pubmed

Left snapshot: By clicking amino acids in the alignment, the respective position in 3D is indicated. Right snapshot: vice versa. In both cases, the rendering style of the picked amino acid or atom can be changed or a text label attached.

Visualization does not require client side Java Why without Java? Java constitutes an additional layer of software and thereby carries an own set of technical problems and risks. A not in-frequent problem is that Java applets simply fail to run. Since January 2014, the message Application Blocked By Security Settings or Your security settings have blocked a local application from running is often exhibited with alignment applets like Jalview. In addition Java bears risks of (I) security threats, (II) browser crashes and (III) memory eating. This was our motivation to develope alignment visualization platform without plugins or Java.


Command line interface

The alignment documents can be generated from the command line using the Strap scripting language.

Graphical user interface

If you prefer a full featured Java user interface, then run the program Strap. In Strap open "To HTML for Web pages ..." in the File-menu.
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