Try population differentiation

 ΦST is under "population comparisons".  

You have three options; 1) Use project distance matrix, 2) Compute distance matrix, or 3) Use conventional F-statistics.  Options 1 or 2 will correspond to  ΦST depending on if you want Arlequin to compute genetic distance or if you are using genetic distances calculated from another program.  For ΦST you will also need to define which model to apply to your dataset for option 2.  Option 3 will be Fst.

Hope this helps

Dear Gaston,

I also met the same question as you. And I am confused by different forms of the parameters. Now, I get a paper which will be useful to decide which parameter is useful for different molecular markers. Please see it in the attached file.

Cheers,

Jie

The problem is that some authors use the term Fst also for Fst analogues such as PhiPT or ΦST. I am looking at the results of my analysis in Arlequin, and I can tell you that the numbers in the genetic distance matrix under the name "Comparisons of pairs of population samples/Population pairwise FSTs" are perfectly the same as those obtained from GenAlex using AMOVA analysis (PhiPT values).