X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=THIRDPARTYLIBS;h=31ad2f5377d02c6afacb9dea78881e16e9adfa16;hb=refs%2Fheads%2Ffeatures%2FJAL-2040_JAL-2137_phyre2;hp=824a6049d3ff2f1362cb1a275b1cdd251c76b7f5;hpb=c2a049dab8f20089e9333141674c55ed4137f9fb;p=jalview.git

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 824a604..31ad2f5 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -10,8 +10,8 @@ ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Mor
 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/
-VARNAv3-91.jar GPL licenced software by Kévin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
+Jmol-14.2.14_2015.06.11.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
@@ -20,6 +20,8 @@ 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
@@ -44,12 +46,16 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 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
 
-Tools not bundled with Jalview source
-jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory.
-