JADE libraries (http://jade.tilab.com/): to construct the multi-agent system
http.jar
iiop.jar
jade.jar
jadeTools.jar
commons-codec-1.3.jar

JFormDesigner libraries (http://www.jformdesigner.com/): optimize construction of Swing GUIs
forms-1.0.7.jar

JDOM libraries (http://jdom.org) : to parse XML files
jdom.jar
xerces.jar
xml-apis.jar

rom-1.0.jar: parsing, generating and publishing RSS and Atom feeds

crimson.jar: to sniff a PARADISE platform with the JAVASniffer tool available in the add-ons of the JADE library

swing-worker-1.1.jar: to perform background tasks with Swing

JLink.jar: to make the link PARADISE-Mathematica

jama.jar: A matrix library, used to substitute bases in Nucleotide3D

AppFramework.jar: the  Swing Application Framework to construct GUIs (https://appframework.dev.java.net/)

swingx.jar: the SwingX project to construct GUIs (http://swinglabs.org/)

To have an embedded Groovy scripting engine:
groovy-1.6.0.jar
jline-0.9.94.jar
antlr-2.7.7.jar
asm-*.jar
commons-cli-1.0.jar

Shell.jar: a library from adiguba (http://adiguba.developpez.com/) to improve the management of external processes

log4j-1.2.15.jar : to handle the loging of messages