Hi Tanmay. For the software Arlequin you need to have a file in extension.arp. You can use the software DNASP (the input file is a fasta file) to define your populations and export the file in .arp extension. You can use that file in Arlequin.

I agree with Martha. Using DNAsp is an easy way to convert fasta format to .arp input files. Alternatively, you can create a template using Arlequin and then insert your haplotypes and the corresponding frequencies into it.