Jalview Readme
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To run application:

java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview

Replace JALVIEW_HOME with the full path to Jalview Installation Directory.

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If you use a proxy server add 

-Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT

If the proxy server requires authentication, add

-Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD