If you used this method, please cite the article: 

Tillier ER, Lui TW (2003) Using multiple interdependency to separate functional
from phylogenetic correlations in protein alignments. Bioinformatics 19: 750–755.

The software availability: http://www.uhnresearch.ca/labs/tillier/depend2/dependency.html

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

Step 2: the following command line was used in our study:

cd /home/lowie/Software/dependency_2.1

./dependency /home/lowie/MatlabCode/Data/Gag_Sequence/FinalSequences/B_Protein/Process_PR_AA_NoGap.fasta 2.58 5 2.58 5 . 1 1

