The Jalview Desktop relies on a number of third-party libraries.
These can be found in the lib directory, with additional compile
time dependencies in the utils directory.

Licencing information for each library is given below:

JGoogleAnalytics_0.3.jar	APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
Jmol-12.1.13.jar	GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
activation.jar	
apache-mime4j-0.6.jar
axis.jar
castor-1.1-cycle-xml.jar
commons-codec-1.3.jar
commons-discovery.jar
commons-logging-1.1.1.jar
commons-logging.jar
httpclient-4.0.3.jar
httpcore-4.0.1.jar
httpmime-4.0.3.jar
jaxrpc.jar
jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012)
jhall.jar
jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
log4j-1.2.8.jar
mail.jar
miglayout-4.0-swing.jar	BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
min-jaba-client.jar
regex.jar
saaj.jar
spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
vamsas-client.jar
wsdl4j.jar
xercesImpl.jar
xml-apis.jar

Additional dependencies

examples/javascript/deployJava.js : http://java.com/js/deployJava.js
examples/javascript/jquery*.js : BSD license
examples/javascript/jshashtable-2.1.js : Apache License