I have to analyse population structure analysis using AFLP data of diploid maize. But while entering the data in STRUCTURE software it isnt taking the data if i enter the ploidy as "2". But goes smooth when while entering it as "1". I m doubtful whether this is correct method or not. Kindly give some proper insight for this.
Regards,
Neha
Ibrahim Celik
Yes this is true because in AFLP data all dominant and recessive alleles are homozygous. So using ploidy level 1 does not effect your results. If you still want to use ploidy level 2, just change input file as 1:1 and 0:0.
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Babak Abdollahi Mandoulakani
Dear Neha
That's right, for dominant scoring, the ploidy level should be entered as 1.
Let me know if I can help more.
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