Hello all I was looking for a software that will collapse 147 sequence into haplotypes. I have tried Skipredundant but somehow it returns much more haplotypes than expected. I have used one threshold of 99%. When I use 90% I get much less haplotypes than expected. To my understanding, every pair of haplotypes that are less similar than the threshold will be kept. Am I doing wrong? Is there another alternative to collapse into haplotypes? Thank you Hanan
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