Hi Yoannis,

yes, I have used the software for haplotype data (13 Plasmodium vivax microsatellites). What exactly is your question? The manual (http://pritch.bsd.uchicago.edu/software/structure22/readme.pdf) is very informative and easy to read. Once you have your data in GenePop format, it is important to make sure you save it in the correct text format (I think it must be a Unix UTF-8 text file).

Have you encountered any other problems?

Hello Cristian,

Thanks for your answear,

I know that the software is suitable for microsatellite data as well as AFLP data and other genotyping techniques. But I wonder if is correct using it for the analysis of sequences such as ITS haplotypes. I've transformed my sequences matrix into a numerical matrix (A=1, T=2, C=3, G=4), then I have used this matrix for runing Structure and it works, but I'm not sure if it is correct since I have not found any reference of such use in the manual nor in any other work.

Hello Yoannis,

OK, I understand now your point. Unfortunately I have never worked with ITS data and thus cannot comment specifically on that. However, the algorithms used by Structure were originally not developed for analysis of haplotypes (but to assess clustering in any type of data). Indeed the program has been used a few times to look for structure in data that has nothing to do with biology (such as language groups). I would thus assume that you can use it for your data - but as said I haven't worked with ITS haplotypes.

Thank you, I didn't know about such use of Structure and I think this knowledge well be useful in any discussion of my work. Anyway I keep looking for a reference, the data transformation like I did is so obvious (if correct) that someone might have used it before, I guess

Thanks Miroslav, I didn't know about BAPS