2 <title>BioJS MSA Viewer Export</title>
5 <strong>Exporting Alignments for viewing with the BioJS MSA
9 Since Jalview 2.9, HTML files can be generated from an alignment
10 within the Jalview desktop application that show the alignment in an
11 interactive viewer called 'BioJS-MSA'. These pages embed Jalview's
12 alignment data as <a href="bioJsonFormat.html">BioJSON</a>, which
13 can be imported back into Jalview, and also interpreted by the BioJS
14 MSA viewer. The BioJS MSA Viewer is a full-featured JavaScript based
15 multiple sequence alignment visualisation system created by a
16 community of biological data visualisation developers, and is
17 developed independently of Jalview.
20 To find out more about the BioJS MSA Viewer, please go to <a
21 href="http://msa.biojs.net/">http://msa.biojs.net/</a>.
25 <strong>Making sure your BioJS MSA export uses the latest
26 BioJS MSA Viewer</strong>
28 <p>In order to allow Jalview to export data with the latest
29 version of the MSA viewer, the Jalview Desktop will download
30 templates for HTML export from our public GitHub Repository.
31 Normally, this should happen without you needing to do anything, but
32 if you do encounter problems, then please get in contact via the
33 jalview-discuss mailing list, or file a bug report.</p>
34 <p>Templates are downloaded to a directory called
35 '.biojs_templates' in your user's home storage space (e.g.
36 ~/.biojs_templates).</p>