Dear Dr. Nawar Dalila

I am only familiar with HWE in GenALEx, so easy to do. Hope it was helpful.

Kind Regards,

Mahmoud

Dear Nawar,

if you used phase, then you haploidised your data, right? If so, you cannot assess the HW equilibrium. At my knowledge, DnaSp treats only haploid data.

regards

Nawar

i assume you cloned your PCR products and then you sequenced from one colony. That way you have haploid phased data. As Ferruccio said, you can not asses whether your polymorphic SNPs are at H-W equilibrium (in order to test HW you need to compare the actual genotypic frequencies to p2, 2pq and q2)

.In case you originally had diploid sequences, it would not be difficult to test HW equilibrium for each polymorphic site. For example, in a simple spreadsheet where you input your observed frequencies and calculate the expected plus the Chi-square tests (1 degree of freedom)

Pablo.

Thanks.... Of course all what you said was completely right, but I supposed that it could be possible to unphase the data directly and calculate the HW. Specially that we enter it as per person per chromosome. But thanks for all the help 

Do not phase the data directly. DnaSp has an option to read diploid data and to phase them using "fastphase": File -> Open Unphase/Genotype data file..

Pablo