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.

A number of sources have also been adapted for incorporation into Jalview's source tree

ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Morris and Nadezhda Doncheva for the Cytoscape StructureViz2 plugin. It is released under the Berkley license and we hereby acknowledge its original copyright is held by the UCSF Computer Graphics Laboratory
 and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081. 
 
 jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util).
 The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code.
 org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java 

Licensing information for each library is given below:

JGoogleAnalytics_0.3.jar	APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
Jmol-14.6.4_2016.10.26.jar	GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
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
commons-net-3.3.jar
groovy-all-2.4.6-indy.jar	APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
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
json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/

quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 

vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html

lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute

lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE

lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE


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
examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php