Jalview Readme
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To run application:

java -classpath "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 use the java runtime bundled with Jalview, then launch jalview like this:

in Windows:
JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview

in Linux:
JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview

in macOS:
JAVA_HOME=JALVIEW_HOME/jre/Contents/Home JALVIEW_HOME/jre/Contents/Home/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview

Note: ensure the -classpath argument is quoted and only use a terminating wildcard (e.g. 'DIR/*') to refer to all jar files in a directory, don't use e.g. 'DIR/*.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