I am facing an issue in doing popgene with AFLP data. As the allele number is very high its creating a problem in creating input files. Can anyone tell me how to create input files for popgene using AFLP data?
Of course in AFLP you get lot of data points. If it is difficult to create input file at a time, divide the gel matrix either 2 or 3 parts or consider only polymorphic data points and mention you get this many data points out of this many are polymorphic and analysis is done using them.
You can input your data as binary matrix in GenAlex software and then you can export this as genepop file. It is option of the software.
http://biology.anu.edu.au/GenAlEx/Welcome.html
Furthermore, you can use this software for population statistics. The analysis is the same with popgene.
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