What kind of data do you have? AFLP's, SSR's, SNP's, DNA sequences? If you are using a codominant data, you could use GenAlEx to export your data to Arlequin. 

thank you Dr. Eric

I have STR sequences

The Arlequin documentation describes in detail how to prepare the input file- have you looked there?  What kind of error are you getting from Arlequin?

Dear Safia, besides GenAlEx, if you have your data on a spreadsheet or genepop format you can also try to use CONVERT (http://www.agriculture.purdue.edu/fnr/html/faculty/rhodes/students%20and%20staff/glaubitz/software.htm) or FORMATOMATIC (http://taylor0.biology.ucla.edu/~manoukis/Pub_programs/Formatomatic/)

If you have any doubt, feel free to ask!

Dear Dr Sean I am not expert in programming so I have this problem of preparing the input 

You really save my life.. the GenAlEX is a genius ;)

Safia,

Arlequin prefers SSRs data as number of repeats instead of the actual lengths of the PCR products. Then, you can perform some more analyses.

If you do not know the size of the flanking sequences, you can just take your lower allele and give it a repeat value of 3 (or 4). Then, you can give the number of repeats to all your other alleles.

Dear Pablo I am not professional in programming so I am looking for the simple way to achieve my statistics

Safia

You don't need to be a professional programmer to do this.If you have your data in a spreadsheet, individuals in column A, and markers in the next columns, just insert a column next to your first SSR data (assuming it is column B2) and type:

=((B2-Size of the flanking sequence)/size of the repeat)

where "Size of the flanking sequence" can be obtained from the literature, or from the smaller allele as I explained previously, and "size of the repeat" will be 2, 3,.4, etc for SSRs with di, tri, tetra-nucleotide repeats.

I don't quite recall, but perhaps software MSA (http://i122server.vu-wien.ac.at/MSA/MSA_download.html) can do it for you