If you used this method, please cite: 

Poon AF, Lewis FI, Frost SD, Pond SLK (2008) Spidermonkey: rapid detection of
co-evolving sites using bayesian graphical models. Bioinformatics 24: 1949–1950.

Software availability: Hyphy v2.1.0 (http://www.hyphy.org/w/index.php/Main Page)

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Here is the option list that our HIV study has used to perform coevolution analysis by Hyphy V2.1.0

(1) standard analysis (you can also find  this option under "Analysis" on top of the window)

(2) select a standard analysis to run - > positive selection -> QuickSelectionDetection.bf

(3) Choose Genetic Code  -> Universal 

(4) New/Restore -> New Analysis

(5) PYPHY Console -> here you pick up your sequence file in Phylip format (nucleotide form). 

(6) Model Options -> Custom ,  then from the input screen, type number: 012345

(7) HYPHY console -> here you pick up your tree trained for the input sequence file 

(8) Save nucleotide model fit to -> just create a random file and save it there, we don't need this output for dN/dS analysis.

(9) dN/dS bias parameter options -> Estimate dN/dS only

(10) Ancestor Counting Options -> BGM co-evolution

(11) Ancestral State Reconstruction and Counting -> Default value

(12) Maximum parents  -> 2
 
(13) Run the MCMC chain for this many interactions  ->   default value (100000)

(14) How many burn-in steps before the main chain   ->   default value (10000)

(15) Sample from each chain      ->   default value (1000)

(16) ancestral sampling -> yes 

(17) How many ancestral samples  -> default value (100) 

(18) Output Options -> Export to File,  then choose the output file you want to save.


