Version 2.9.0b1

Jalview is free to end-users because of support from the UK's BBSRC and The Wellcome Trust

If you would like to see Jalview continue to be available then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to: by Friday 19th October 2018.

Thank you all those who have already written such nice letters!

Version Date: 

New Features


  • Updated Spanish translations of localized text for 2.9


  • Signed OSX InstallAnywhere installer
  • Support for per-sequence based annotations in BioJSON


  • Split frame example added to applet examples page

Issues Resolved


  • Annotations corrupted after BioJS export and reimport
  • Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'
  • Incorrect warning about deleting all data when deleting selected columns
  • Patch to build system for shipping properly signed JNLP templates for webstart launch
  • EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing
  • Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly
  • Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug
  • Split cDNA/Protein view position and geometry not recovered from jalview project
  • Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view
  • Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON


  • Reorder sequences mirrored in cDNA/Protein split frame
  • Applet with Jmol examples not loading correctly


  • Mapping of cDNA to protein in split frames incorrect when sequence start > 1
  • Broken images in filter column by annotation dialog documentation
  • Feature colours not parsed from features file
  • Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description