Please, is there anybody to give me a hint? I am really stuck in this topic..
I do not understand why Arlequin and DNAsp provide different results for the same data set (cpDNA-sequences from 122 individuals, 3248bp, S = 8, pi = 1.25).
For Tajima's D the results from both programs are essentially the same (D= - 0.361; P = 0.4).
However, Fu's Fs in Arlequin is very negative & significant (Fu's Fs = -28.988; P = 0.000),
but in DNAsp it is not so negative and insignificant (Fu's Fs = -0.09655; P[sim
Hey, I had the same problem and tried different things. And was thinking about the same like you. Maybe it is caused by gaps. I figured out that DNASP is automatically cutting the positions with missing data from the alignment (for example caused by shorter sequences). So the analysed alignment has not the full length. Arlequin is automatically analysing the full alignment. To receive the same results as calculated with DNASP you need to tell Arlequin to exclude the missing data (like you say). I am creating my arelquin files with DNASP. So before saving as arlequin file you can set the option that you want to analyse just the positions with information for all sequences (for example from base 5-655) :) This way I am getting the same results for both. But which one (full length or not) is the best to use - I don't know. Best, Kati
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