here is a working file that you can load into arlequin. Things that you can tweak here:

line 9, here you are saying how many groups do you have

line 17, from here you are giving name to each group

line 18, from here you are giving the number of sequences in the group

for each group you can just paste your sequences in the form:

name_of sequence number_of_occurences DNA_sequence

just copy paste your data to fit the structure in the file. I suggest using sublime text 2 for multiple select and doing the text manipulations

At the end of the file once again you have to write down all of the groups that you have in your file, rest of the manipulation can be done from the arlequin itself

Dear sir, agoIreneusz Stolarek , thanks for your valuable answer, but my data is not sequence data. My data is RFLP data which have only cut sites.

Example: AA= WILD TYPE, AG=HETEROZYGOUS MUTANT, GG= MUTANT.

Dear sir, Artur Burzynski, thanks for your question. I am working on specific region of the particular gene. Its a fragment sizes. Here I have uploaded the excel file, please find the attachment. It is possible to make arlequin input file from this excel file?

Thank you very much sir, Artur Burzynski , i will go through manual.

Find the following sites useful

http://www.peter.unmack.net/molecular/programs/arlequin.make.input.html

https://faculty.eeb.ucla.edu/Barber/Web%20Protocols/Arlequin.pdf

Dnasp is more effective for haplotype analysis. Make the input file in fasta format and perform haplotype analysisin Dnasp.The haplotype network can be drawn by transferring the haplotype analysis data to Network software. Or you can export the data from Dnasp to arlequin as well.

I have SSR's data how can i put this data in Arlequin ? i want to calculate gene diversity from the same ....