Jalview Readme
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The source is available as a tar file and comes complete with the GNU General Public License. 

To build the application you will need a J2SDK 1.4+. 

An Ant build file (build.xml) is provided, you will need to install Apache Ant first. 
Run ant to view usage which will display a list of useful build targets.

You can also use Borland JBuilder to build Jalview. A JBuilder project file (JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided.

For more help, read the file doc/building.html


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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