Jalview 2.6

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New Features


  • Support for Java bioinformatics analysis web services (JABAWS)
  • Web Services preference tab
  • Analysis parameters dialog box and user defined preferences
  • Improved speed and layout of Envision2 service menu
  • Superpose structures using associated sequence alignment
  • Export coordinates and projection as CSV from PCA viewer


  • enable javascript: execution by the applet via the link out mechanism


  • Updated the Jmol Jalview interface to work with Jmol series 12
  • The Jalview Desktop and JalviewLite applet now require Java 1.5
  • Allow Jalview feature colour specification for GFF sequence annotation files
  • New ‘colour by label’ keword in Jalview feature file type colour specification
  • New Jalview Desktop Groovy API method that allows a script to check if it being run in an interactive session or in a batch operation from the Jalview command line

Issues Resolved

  • clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column


  • typo in AlignmentFrame->View->Hide->all but selected Regions menu item
  • sequence fetcher replaces ‘,’ for ‘;’ when the ‘,’ is part of a valid accession ID
  • fatal OOM if object retrieved by sequence fetcher runs out of memory
  • unhandled Out of Memory Error when viewing pca analysis results
  • InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update)
  • Installanywhere Jalview silently fails to launch


  • Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.