DNAsp is useful too. I use this software on windows 8.

You can likewise try Species Identifier.

Information on statistics made by the Software can be found in Meier, R., Kwong, S., Vaidya, G., Ng, Peter K. L. (2006) DNA Barcoding and Taxonomy in Diptera: a Tale of High Intraspecific Variability and Low Identification Success. Systematic Biology, 55: 715-728

you have the Advantage of not getting only mean values (see davids answer)

Thanks to all for valuable suggestion, papers and softwares.

You can use ExCaliBar a simple and user friendly software, which calculate intra and interspecific distances in separate column. You can download it from: http://datadryad.org/resource/doi:10.5061/dryad.r458n.

Thanks for the software.

• Hi Mahmoudi, i tried Excalibar and i only get interspecific distances not intraspecific distances. Please guide me how to prepare file for Excalibar.

You can also use Arlequin. It's very easy to use and works wonders with the output from DNAsp. First you asign sequences to the different species then you get an haplotype file which Arlequin uses to create a distance matrix, giving you intraspecific (diagonal) and interspecific distances.

http://cmpg.unibe.ch/software/arlequin35/

Thanks Daniel.

Dear Ali,

Have you received my message about ExCaliBar?

Could you manage to run the software?

Best,

Ahmad

Dear Mahmoudi,

Yes i received  your message . I tried it but i only get interspecific distances and xcel sheet for intraspecific distances only show names.