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 1.5+. 

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 may also be able to use Borland JBuilder to build Jalview. A JBuilder project file 
(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided, 
but the library dependencies are almost certainly out of date. See the build.xml 
for current dependencies.

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