Arlequin Input Format

Question

[Carl]

Hi everyone,

I am having problems with Arlequin, since its guide it's not very clear.. How do I create a proper input file? I have SNPs data concerning 500 individuals belonging to 5 different populations.

I would really appreciate any help. Thank you very much.

[fu_entomology]

Hi Carl,

Did you solve the problem? I am facing the same issue? What was your original format of SNP data? VCF?

Cheers

Answer 1

[Shicheng Guo]

You can download the following perl script to transfer ped file to Arlequin input file: https://www.dropbox.com/s/nd45vy42x09tde8/transformation.pl?dl=0

Answer 2

[kumar.vinod81]

I dont have SNP input format for Arlequin, but earlier I've worked with RAPD and SSR in Arlequin, if you think it ca help you, reply. Thanks

[Carl]

Hi and thank you for your help. Actually I think it could be useful: how did you write the input for RAPD (1-0 or DNA sequences)? Maybe I can create the SNPs input file from PLINK, using the --recode12 option

[kumar.vinod81]

RAPD data in binary (1,0) format. Thanks,

Answer 3

[liran0921]

I couldn't remember exactly, but there should be some example files provided by Arlequin which you can use to create you own input file.