Jalview 2.8

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.8 (without auto-updates).

To revert back to the Jalview RELEASE channel, please visit the Using the Jalview Launch file page.

Download the Jalview Launch file (.jvl) for version 2.8?


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 (http://varna.lri.fr) 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