I have a little experience with Arlequin and just remember that preparation of input file is quite a problem. Alternatively you can use other software, like Genepop (available online) to calculate Fst. And my guess for data type is SNP allele frequences.

Hi Linda,

I had the same problem with the preparation of the imputs files for Arlequin. But I found a program called DnaSPv5. This program allows you to export directly in *arp format for Arlequin (the haplotype frequencies).

The reference is:

Librado P. and Rozas J. (2009) DnaSPv5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452

I hope it will be helpful for you

Dear Linda,

Arlequin can manage different datasets (sequences, frequencies, dominant data, etc.). There are some programs that make conversion to .arp files. One is DnaSp, as David already mentioned; DnaSp can manage only DNA sequences. For allele frequencies of  codominant markers, you can use Genalex (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html). The last version of GENEPOP can also make conversions to .arp files. Another interesting program is CONVERT (Glaubitz JC -2004- CONVERT: a user friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4: 309-310), that makes a number of conversions to different format files.

I hope this information can be of help for you.

Ciao

Dear all, I have data in SNP barcode format for 3 different populations.I am trying to calculate Fst (genetic difference/distance) among the populations but can't seem to find my way around it. Is there any online software I can upload my SNP data into,I tried Genepop but couldn't make any headway. Can anyone help,please?