Jalview 2.10.5

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.10.5 (without auto-updates).

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Jalview 2.10.5 is a minor release that includes critical patches for users working with Ensembl, RNA secondary structure annotation, and those running Jalview on OSX with Java 10.

New Features

  • Default memory for Jalview webstart and InstallAnywhere increased to 1G.
  • Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the Format menu, or for command-line use via a Jalview properties file.
  • Ensembl client updated to Version 7 REST API and sequence data now imported as JSON.
  • Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property.


  • Support added to execute test suite instrumented with Open Clover

Issues Resolved

  • Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment.
  • Annotation obscures sequences if lots of annotation displayed.
  • Group conservation/consensus not shown for newly created group when ‘Apply to all groups’ selected
  • Corrupted display when switching to wrapped mode when sequence panel’s vertical scrollbar is visible.
  • Alignment is black in exported EPS file when sequences are selected in exported view.
  • Groups with different coloured borders aren’t rendered with correct colour.
  • Jalview could hang when importing certain types of knotted RNA secondary structure.
  • Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1.
  • ‘.’ inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile.
  • Jalview annotation rows containing upper and lower-case ‘E’ and ‘H’ do not automatically get treated as RNA secondary structure.
  • .jvp should be used as default extension (not .jar) when saving a Jalview project file.
  • Mac Users: closing a window correctly transfers focus to previous window on OSX

Java 10 Issues Resolved

  • OSX - Can’t save new files via the File or export menus by typing in a name into the Save dialog box.
  • Jalview now uses patched version of the VAqua5 ’look and feel’ which has improved compatibility with the latest version of OSX.