You can use this tool : Microsatellite tool kit.

Here is the link:

http://genome-lab.ucdavis.edu/Links/Pop_Genet_ECL290/Week-1/download%20micro-toolkit.htm

Your file should be in spreadsheet (excel).Select data format "FSTAT".

Save it as filename.dat.All the best

Thank you Gaurav Pandey but i think this tool not useful for my mtDNA sequences. It is only useful for Microsatellite data.

The dna sequences can be converted from FASTA format to any format using PGDSpider version 2.0.6.0 software( download link: http://www.cmpg.unibe.ch/software/PGDSpider/).

For online softwares, reffer link below: Remember input data must be in genpop/ text format.

http://genepop.curtin.edu.au/genepop_op7.html

(fore more help:http://genepop.curtin.edu.au/Option7.html)