I read a recommendation of how to find non-duplicated chromosomes: using JGAp (genetic algorithm library) and the duplicated chromosomes
How do you find a chromosome with non-repeated alleles using JGAP?
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I have been thinking about this problem recently too...
My current solution is simply to include a large penalty in the fitness function of my genetic algorithm, when the chromosome contains duplicate alleles.
Whilst I imagine there are better ways of approaching this problem, this seems to be working - for my purposes at least..