Jalview 2.8.2

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New Features


  • Updated Java code signing certificate donated by Certum.PL.
  • Features and annotation preserved when performing pairwise alignment
  • RNA pseudoknot annotation can be imported/exported/displayed
  • ‘colour by annotation’ can colour by RNA and protein secondary structure
  • Warn user if ‘Find’ regular expression is invalid (mentioned post-hoc with 2.9 release)


  • Extract and display secondary structure for sequences with 3D structures
  • Support for parsing RNAML
  • Annotations menu for layout
    • sort sequence annotation rows by alignment
    • place sequence annotation above/below alignment annotation
  • Output in Stockholm format
  • Internationalisation: improved Spanish (es) translation
  • Structure viewer preferences tab
  • Disorder and Secondary Structure annotation tracks shared between alignments
  • UCSF Chimera launch and linked highlighting from Jalview
  • Show/hide all sequence associated annotation rows for all or current selection
  • disorder and secondary structure predictions available as dataset annotation
  • Per-sequence rna helices colouring
  • Sequence database accessions imported when fetching alignments from Rfam
  • update VARNA version to 3.91
  • New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
  • Command line argument to set default JABAWS server
  • include installation type in build properties and console log output
  • Updated Jalview project format to preserve dataset annotation

Issues Resolved


  • Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
  • Raise dialog box if user deletes all sequences in an alignment
  • Pressing F1 results in documentation opening twice
  • Sequence feature tooltip is wrapped
  • Double click on sequence associated annotation selects only first column
  • Redundancy removal doesn’t result in unlinked leaves shown in tree
  • Undos after several redundancy removals don’t undo properly
  • Hide sequence doesn’t hide associated annotation
  • User defined colours dialog box too big to fit on screen and buttons not visible
  • author list isn’t updated if already written to Jalview properties
  • Popup menu won’t open after retrieving sequence from database
  • File open window for associate PDB doesn’t open
  • Left-then-right click on a sequence id opens a browser search window
  • Cannot open sequence feature shading/sort popup menu in feature settings dialog
  • better tooltip placement for some areas of Jalview desktop
  • Allow addition of JABAWS Server which doesn’t pass validation
  • Web services parameters dialog box is too large to fit on screen
  • Muscle nucleotide alignment preset obscured by tooltip
  • JABAWS preset submenus don’t contain newly defined user preset
  • MSA web services warns user if they were launched with invalid input
  • Jalview cannot contact DAS Registy when running on Java 8
  • 'Superpose with' submenu not shown when new view created

Deployment and Documentation

  • 2G and 1G options in launchApp have no effect on memory allocation
  • launchApp service doesn’t automatically open www.jalview.org/examples/exampleFile.jar if no file is given
  • InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available

Application Known issues

  • corrupted or unreadable alignment display when scrolling alignment to right
  • retrieval fails but progress bar continues for DAS retrieval with large number of ID
  • flatfile output of visible region has incorrect sequence start/end
  • rna structure consensus doesn't update when secondary structure tracks are rearranged
  • invalid rna structure positional highlighting does not highlight position of invalid base pairs
  • out of memory errors are not raised when saving Jalview project from alignment window file menu
  • Switching to RNA Helices colouring doesn't propagate to structures
  • colour by RNA Helices not enabled when user created annotation added to alignment
  • Jalview icon not shown on dock in Mountain Lion/Webstart

Applet Known Issues

  • JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
  • Jalview and Jmol example not compatible with IE9
  • Sort by annotation score doesn’t reverse order when selected