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. 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/ 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