Please cite the following reference, if you use CoMap:

Dutheil J, Pupko T, Jean-Marie A, Galtier N (2005) A model-based approach for
detecting coevolving positions in a molecule. Molecular biology and evolution 22:
1919–1928.

Software availability: http://gna.org/projects/comap
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%% step 1: install the comap software according to its manual

%% step 2: perform the coevolution analysis:
The following command lines are used in our HIV study

cd /home/lowie/Software/CoMap-1.4.0/bin

./comap input.sequence.file=/home/lowie/MatlabCode/Data/Gag_Sequence/Coevolution/CoMap/PR_CoMapAA.fasta input.tree.file=/home/lowie/MatlabCode/Data/Gag_Sequence/PhylogeneticTree/RAxML_result.PRComap statistic.output.file=/home/lowie/MatlabCode/Data/Gag_Sequence/Coevolution/CoMap/PR_CoMapPredicted.txt nijt_aadist.sym=no nijt=aadist nijt_aadist.type=grantham model=LG08 alphabet=Protein analysis=pairwise input.sequence.format=Fasta statistic=Compensation statistic.null=yes statistic.null.compute_pvalue = yes statistic.null.nb_rep_CPU=8  statistic.min=0

