Version 2.8

Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported 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 22nd March 2019.

Thank you!

Version Date: 


New Features


  • Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
  • JABAWS server status indicator in Web Services preferences
  • VARNA ( viewer for RNA structures in Jalview alignment window
  • Updated jalview build and deploy framework for OSX mountain lion, windows 7, and 8
  • Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes
  • Improved sequence database retrieval GUI
  • Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs')
  • Jalview project improvements
    • Store and retrieve the 'belowAlignment' flag for annotation
    • calcId attribute to group annotation rows on the alignment
    • Store AACon calculation settings for a view in Jalview project
  • horizontal scrolling gesture support
  • Visual progress indicator when PCA calculation is running
  • Simpler JABA web services menus
  • visual indication that web service results are still being retrieved from server
  • Serialise the dialogs that are shown when jalview starts up for first time
  • Jalview user agent string for interacting with HTTP services
  • DAS 1.6 and DAS 2.0 source support using new JDAS client library
  • Examples directory and Groovy library included in InstallAnywhere distribution


  • RNA alignment and secondary structure annotation visualization applet example


  • Normalise option for consensus sequence logo
  • Reset button in PCA window to return dimensions to defaults
  • Allow seqspace or Jalview variant of alignment PCA calculation
  • PCA with either nucleic acid and protein substitution matrices
  • Allow windows containing HTML reports to be exported in HTML
  • Interactive display and editing of RNA secondary structure contacts
  • RNA Helix Alignment Colouring
  • RNA base pair logo consensus
  • Parse sequence associated secondary structure information in Stockholm files
  • HTML Export database accessions and annotation information presented in tooltip for sequences
  • Import secondary structure from LOCARNA clustalw style RNA alignment files
  • import and visualise T-COFFEE quality scores for an alignment
  • 'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation
  • New Jalview Logo

Documentation and Development

  • documentation for score matrices used in Jalview
  • New Website!


Issues Resolved


  • PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service
  • Stop windows being moved outside desktop on OSX
  • Filetype associations not installed for webstart launch
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
  • revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
  • Jalview 2.7 is incompatible with Jmol-12.2.2
  • View all structures superposed fails with exception
  • Jnet job queues forever if a very short sequence is submitted for prediction
  • Cut and paste menu not opened when mouse clicked on desktop window
  • Putting fractional value into integer text box in alignment parameter dialog causes jalview to hang
  • Structure view highlighting doesn't work on windows 7
  • View all structures fails with exception shown in structure view
  • Characters in filename associated with PDBEntry not escaped in a platform independent way
  • Jalview desktop fails to launch with exception when using proxy
  • Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty
  • Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
  • DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
  • Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
  • Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
  • Cannot close news reader when JABAWS server warning dialog is shown
  • Option widgets not updated to reflect user settings
  • Edited sequence not submitted to web service
  • Jalview 2.7 Webstart does not launch on mountain lion
  • InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
  • Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment
  • Sequence associated annotation rows not associated when loaded from jalview project
  • Browser launch fails with NPE on java 1.7
  • JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
  • NPE with v2.7 example when clicking on Tree associated with all views
  • Exceptions when copy/paste sequences with grouped annotation rows to new window


  • Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
  • loading features via javascript API automatically enables feature display
  • scrollToColumnIn javascript API method doesn't work


  • Redundancy removal fails for rna alignment
  • PCA calculation fails when sequence has been selected and then deselected
  • PCA window shows grey box when first opened on OSX
  • Letters coloured pink in sequence logo when alignment coloured with clustalx
  • Choosing fonts without letter symbols defined causes exceptions and redraw errors
  • Initial PCA plot view is not same as manually reconfigured view
  • Grouped annotation graph label has incorrect line colour
  • Grouped annotation graph label display is corrupted for lots of labels