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

Related JDOM libraries to do XPath:
jaxen.jar
saxpath.jar

rome-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

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-1.7.0.jar
jline-0.9.94.jar
antlr-2.7.7.jar
asm-*.jar
commons-cli-1.0.jar

log4j-1.2.15.jar : to handle the loging of messages. Used by several frameworks

JAX-WS to connect SOAP web services (https://jax-ws.dev.java.net/):
jaxb-api.jar
jaxb-impl.jar
jaxb-xjc.jar
mimepull.jar
resolver.jar
saaj-api.jar
saaj-impl.jar
stax-ex.jar
woodstox.jar
jaxws*.jar
jsr*.jar
FastInfoset.jar
activation.jar

wspv.jar: to consume the PseudoViewer WebService

AXIS to connect SOAP web services:
axis.jar
saaj.jar
jaxrpc.jar
wsdl4j-1.5.1.jar
commons-discovery-0.2.jar
commons-logging-1.0.4.jar

commons-io-1.4.jar: Collection of I/O utilities from the Apache Commons project