If you used this method, please cite the article: 

Yeang CH, Haussler D (2007) Detecting coevolution in and among protein domains.
PLoS computational biology 3: e211.

Software availability:  http://www.stat.sinica.edu.tw/chyeang/

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Step 1: dowload the software and install it according to the manual.

Step 2: perform the coevolution analysis
Here is the command line used in our HIV study 

cd /home/lowie/Software/Coevolution/CTMP/

./calculate_likelihood 1 0 Process_PR_AA_NoGap_AA_VariedPosition.phy - RAxML_result.PRCTMP - Process_PR_AA_NoGap_ID.txt RAxML_result.PRCTMP Process_PR_AA_NoGap_Gene.txt - aa_prior.txt aa_ratemat.txt 0.7 0.99 0.99 0.01 1.0 Process_PR_AA_NoGap_coev_pairs.txt 0


