3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>BioJSON in Jalviwe</title>
27 <strong>BioJSON support in Jalview</strong>
29 <p>BioJSON is a JavaScript Object Notation (JSON) specification
30 for the representation and exchange of multiple sequence alignment
32 <p>Jalview 2.9 includes support for reading and writing BioJSON
33 v1.0 data directly, or embedded in HTML documents. It can also
34 generate HTML pages which employ the <a href="biojsmsa.html">BioJS MSA viewer</a> for
35 interactive display of BioJSON data.</p>
37 <strong>Finding out more about BioJSON</strong>
40 The BioJSON specification is published at <a
41 href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
44 <strong>Jalview's Support for BioJSON v1.0</strong>
46 <p>BioJSON exports of an alignment view include
47 the following additional data:</p>
49 <li>Alignment Annotations</li>
50 <li>Alignment Features</li>
51 <li>Alignment Sequences</li>
53 <li>Hidden Columns</li>
54 <li>Hidden Sequences</li>
55 <li>Sequence Groups</li>
57 <p>The following data are NOT currently preserved on export:</p>
59 <li>Alignment Reference sequences</li>
60 <li>Representative sequence groups</li>
62 <li>3D Structures</li>