Privacy for Jalview Users
The Jalview Desktop application available from the www.jalview.org site does not contain code that is designed to collate any personal or private information without your consent. However, the application does contain routines which contact a variety of web services, and some of these are specifically designed to assess who is using Jalview. We collect usage statistics in the following ways:

• HTTP logs on the Jalview website
  We record IP addresses of machines which access the web site, either via the browser when downloading the application, or when the Jalview Desktop user interface is launched.
  • The JNLP file at www.jalview.org/webstart/jalview.jnlp is retrieved to determine if you are running the latest version of Jalview.
  • The questionnaire web service at www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique cookie for the current questionnaire is stored in the Jalview properties file.
  • The Jalview web services stack is contacted to retrieve the currently available web services. All interactions with the public jalview web services are logged, but we delete all job data (input data and results) after about two weeks.
• Google Analytics
  Since jalview 2.4.0b2, the Jalview Desktop records usage data with Google Analytics via the JGoogleAnalytics class.
  The Google Analytics logs for Jalview version 2.4 only record the fact that the application was started, but in the future, we will use this mechanism to improve the Desktop user interface, by tracking which parts of the user interface are being used most often.

Stopping Jalview from calling home If you run Jalview in 'headless mode' via the command line, then the program shouldn't try to contact any of the web servers mentioned above (if it does, then its a bug!). You can also specify some command line options to disable the questionnaire and usage statistics check. Finally, the Connections Tab of the jalview preferences contains options for controlling the submission of usage statistics. Other Web Clients in Jalview
The Jalview desktop is intended to make it easier to interact with web-based bioinformatics resources, but we cannot vouch for the integrity of any of the services you might access via the program. You can turn this off your machine to the outside world. You may voluntarily submit query text