

welcome to hyphy
option list: 
(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 -> Single Ancestor Counting

(11) SLAC options -> Full tree

(12) Treatment of Ambiguities  -> Averaged 
 
(13) Test Statistic -> Approximate 

(14) from the screen window, significance level for a site to be classified as positively/negatively selected , type : 0.05

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


