Exporting Alignments for viewing with the BioJS MSA Viewer

Since Jalview 2.9, HTML files can be generated from an alignment within the Jalview desktop application that show the alignment in an interactive viewer called 'BioJS-MSA'. These pages embed Jalview's alignment data as BioJSON, which can be imported back into Jalview, and also interpreted by the BioJS MSA viewer. The BioJS MSA Viewer is a full-featured JavaScript based multiple sequence alignment visualisation system created by a community of biological data visualisation developers, and is developed independently of Jalview.

To find out more about the BioJS MSA Viewer, please go to http://msa.biojs.net/.

Making sure your BioJS MSA export uses the latest BioJS MSA Viewer

In order to allow Jalview to export data with the latest version of the MSA viewer, the Jalview Desktop will download templates for HTML export from our public GitHub Repository. Normally, this should happen without you needing to do anything, but if you do encounter problems, then please get in contact via the jalview-discuss mailing list, or file a bug report.

Templates are downloaded to a directory called '.biojs_templates' in your user's home storage space (e.g. ~/.biojs_templates).