BioJSON support in Jalview

BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of multiple sequence alignment data.

Jalview 2.9 includes support for reading and writing BioJSON v1.0 data directly, or embedded in HTML documents. It can also generate HTML pages which employ the BioJS MSA viewer for interactive display of BioJSON data.

Finding out more about BioJSON

The BioJSON specification is published at http://jalview.github.io/biojson/.

Jalview's Support for BioJSON v1.0

It is currently possible to export an alignment view along with the following additional data:

• Alignment Annotations
• Alignment Features
• Alignment Sequences
• Color Scheme
• Hidden Columns
• Hidden Sequences
• Sequence Groups

Jalview data not supported in BioJSON v1.0

The following data are not currently preserved on export:

• Alignment Reference sequences
• Representative sequence groups
• Trees
• 3D Structures