Jalview Readme
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To run application:

java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar [-help ... ]

Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
Use -help to see the available command line arguments.

For best results use a Sun java run time environment (not the gcj gnu java, sorry!). 

If you want to the java runtime bundled with Jalview, then launch jalview like this:

JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar 

Please Note: the -jar jalview.jar option launches the jalview.bin.Jalview class in the jalview.jar
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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