Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site. Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings. In this case it may pop up a window asking for proxy settings. If this does not happen, and proxy settings are required, you can create a file called

proxy.txt

that should contain your proxy host and port like this:

host=your.proxyhost.com
port=3128

You should put the file in the same folder as the file getdown.txt:

• In Windows this is the folder you installed Jalview into (by default this is %APPDATA%\Local\Jalview)
• In macOS this is buried in the Jalview application bundle as Contents/Resources/app (by default /Applications/Jalview.app/Contents/Resources/app/)
• In Linux this is also the folder you installed Jalview into (by default this is ~/opt/jalview/).

The current release (2.11.1.0) does not pass settings from this file on to the Jalview application. This will be fixed in a future release. In the meantime you can configure the proxy for Jalview in Jalview’s own Preferences (see Tools->Preferences->Connections).