Package files:
. mll.jar - programs only
. mllwithdata.jar - both programs and data

Installation:
. Unpackage all files into an empty base directory:
  jar -xvf mll.jar
  OR
  jar -xvf mllwithdata.jar
. The packages require Apache Ant (http://ant.apache.org/) and the Contrib tasks (http://sourceforge.net/projects/ant-contrib) to run. Install them if not already installed in your system.

To run (with data):
At the base directory, run the ant task "run":
ant run

Data files required for running the programs:
data/ppi/ready/proteins.txt: list of protein names, one protein per line
data/ppi/ready/proteinKernel.txt: protein kernel in tab-delimited format
data/ppi/ready/goldPosProteinPairs.txt: tab-delimited gold-standard positive protein pairs, one pair per line
data/ppi/ready/goldNegProteinPairs.txt: tab-delimited gold-sntadard negative protein pairs, one pair per line
data/ddi/ready/domains.txt: list of domain instances, one instance per line, in format <protein><tab><domain family>
data/ddi/ready/domainKernel.txt: domain instance kernel in tab-delimited format
data/ddi/ready/MediatingKernel.txt: extra mediating kernel for paradigms 2 and 3
data/ddi/ready/goldPosDomainPairs.txt: tab-delimited gold-standard positive domain instance pairs, one pair per line
data/ddi/ready/goldNegDomainPairs.txt: tab-delimited gold-standard negative domain instance pairs, one pair per line
data/rri/ready/residues.txt: list of residues, one residue per line, in format <protein><tab><domain family><tab><residue id>
data/rri/ready/residueKernel.txt: residue kernel in tab-delimited format
data/rri/ready/goldPosResiduePairs.txt: tab-delimited gold-standard positive residue pairs, one pair per line
data/rri/ready/goldNegResiduePairs.txt: tab-delimited gold-standard negative residue instance pairs, one pair per line

To analyze the results:
At the base directory, run the an task "analyze":
ant analyze
The reported values are in the column "AUC (all)"