I am working on a population statistics project and have autosomal STR allele frequencies for 10 loci for 29 populations and was trying to figure out how the Arlequin input file had to be formatted for this. The manual mentions the format for allele frequency data, but not what to do if you have multiple loci. I have seen other papers mention using Arlequin for this purpose to perform linkage testing and AMOVA analysis, amongst other tests, but can't find anything about how to set up the input file. Any help would be greatly appreciated.
I hope you have more than frequencies. You need individual genotypes, to perform an AMOVA test. If you have individual genotypes, it is worthwhile to enter these into GenAlEx and then export to all sort of other software afterwards, or even just do the AMOVA inside GenAlEx. Good luck Per
Hello Nathan,
At the moment, I am facing the same issue you described. I'm working with allelic frequencies of STR for 15 loci and I want to perform comparative analyses with over 30 populations. As you mention, the papers I've reviewed also indicate the use of the software Arlequin. Have you been able to find the required format by now, or did you have to opt for another program and format? I would greatly appreciate your assistance with this matter.
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