Jalview 2.2.1

Hello all Jalview users,

The latest update to Jalview, version 2.2.1 is now available from


This is mainly a bug fix release, fixing various image output, annotation input/output bugs which have been reported since Jalview 2.2.

You will also find the new version prompts the user to answer a short questionnaire. Once this has been completed, or if you click the button "Dont show me this again" you will not be asked again.

*** Applet developers please note the critical bug pointed where the applet fails and crashes the web browser for several Linux OS using Java 1.6. The problem was due to a font library loading issue in Java 1.6 for the main menu bar. This issue has been resolved in the latest applet. ***

As well as the bug fixes there are a few new features added in the new version:

Non standard characters can be read and displayed.

Annotations/features can be loaded/exported from the applet via the textbox.

The applet allows the editing of sequence names, annotation names and group names.

Several new public methods are available for the applet to import/export annotations, features and alignments.

A new Preference setting in the main application to display sequence name font as italic or not, also the overview window can be displayed for all new alignment windows.

The annotation file format has been extended to allow Sequence_groups to be defined.

Bye for now,

The Jalview Team.