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: j8lib: activation.jar apache-mime4j-0.6.jar axis.jar biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE commons-codec-1.3.jar Apache license - https://www.apache.org/licenses/ commons-discovery.jar Apache license - https://www.apache.org/licenses/ commons-logging-1.1.1.jar Apache license - https://www.apache.org/licenses/ flatlaf-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license flatlaf-extras-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE groovy-all-2.4.21-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip htsjdk-2.23.0.jar built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute httpclient-4.0.3.jar httpcore-4.0.1.jar httpmime-4.0.3.jar intervalstore-v1.1.jar jabaws-min-client-NO_LOG4J-2.2.1.jar Apache license - pre-release of JABAWS 2.2.1 client built from https://source.jalview.org/crucible/changelog/jabaws?cs=586260b9f877e0954513fcffb0aa27eaddc5d0ff java-json.jar jaxrpc.jar jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html jetty-http-9.2.10.v20150310.jar jetty-io-9.2.10.v20150310.jar jetty-server-9.2.10.v20150310.jar jetty-util-9.2.10.v20150310.jar jfreesvg-3.4.3.jar GPL v3 licensed library from the JFree suite - last release with Java 1.8 compatibility http://www.jfree.org/jfreesvg/ JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ jhall.jar Jmol-NO_LOG4J-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile) 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) jsoup-1.8.1.jar jsr311-api-1.1.1.jar jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 log4j-api-2.17.1.jar Apache license version 2.0 log4j-core-2.17.1.jar Apache license version 2.0 log4j-slf4j18-impl-2.17.1.jar Apache license version 2.0 mail.jar miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt regex.jar saaj.jar servlet-api-3.1.jar slf4j-api-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/ slf4j-nop-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/ vamsas-client.jar VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr wsdl4j.jar xercesImpl.jar xml-apis.jar Libraries for Test Suite utils/axis-ant.jar utils/ant-contrib-1.0b3.jar utils/hamcrest-core-1.3.jar utils/roxes-ant-tasks-1.2-2004-01-30.jar utils/proguard_5.3.3.jar utils/jhindexer.jar utils/junit-4.12.jar utils/jhall.jar utils/classgraph-4.1.6.jar BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6 utils/testnglibs/guava-base-r03.jar utils/testnglibs/guava-collections-r03.jar utils/testnglibs/bsh-2.0b4.jar utils/testnglibs/snakeyaml.jar utils/testnglibs/testng-sources.jar utils/testnglibs/testng.jar utils/testnglibs/junit-4.12.jar utils/testnglibs/jcommander.jar utils/wsdl4j.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 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php New in j11lib: FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE groovy-*2.5.7.jar Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html istack-commons-runtime.jar CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html javax.activation-api-1.2.0.jar CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt javax.annotation-api-1.3.2.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE javax.jws-api-1.1.jar CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html javax.servlet-api-4.0.1.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1 javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1 javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1 jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php txw2-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php wsdl4j-1.6.3.jar CPL - http://www.opensource.org/licenses/cpl1.0.txt