Version 2.6

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 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.