If you used this software, please cite the paper: 

Burger L, van Nimwegen E (2010) Disentangling direct from indirect co-evolution
of residues in protein alignments. PLoS computational biology 6: e1000633.

Software availability: please request the software from the authors: lukas.burger@fmi.ch, 

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Step 1: install the software according its manual

Step 2: command lines used in our HIV study: 

cd /home/lowie/Software/PredictContactPrior/

perl runContactPredictions.pl /home/lowie/EnsembleCoevolutionSystem/Dataset/Process_PR_AA_NoGap.fasta


