You may try POPGENE. With it you can generate dendrogram of sub-populations or groups. https://www.ualberta.ca/~fyeh/popgene_download.html

Thank you Madhav, I've tried POPGENE as well, but the dendrogram is not nice and I also have to  replace each popoulation with it's real name. That's why I'm looking for another software.

You may also use R software.

Hi,

Your choice of the softwares is depend on the parameters you wish to calculate and the objectives of your study. if you wish to calculate diversity parmeters POPGENE can be a option. For within and among population diversity and PCoA you can use GeneAlex or ALEREQUIN. For Dendrogram construction You can use PHYLIP/ DARWIN/ Tree/Population Software. And If you wish to evaluate population structure then go for STRUCTURE software. With best wishes

Arun

Hi Arun,

Actually It was for Dendrogram construction and I found the soluation with MEGA, which was very helpeful as well. Thank you for your answers. 

Hi Chaima

XLSTAT is better and easy to use for construction of dendrogram

regrads

Hi,ClusterVIs software, it's very easy to use  for construction of dendrogram.

Regards

Hi....

You can try MSA to compute the genetic distances and then any other software which accepts these distances, for the dendrogram construction, according to the data input format.

Regards