[EMBOSS] Skipredundant problems

[Hanan Sela]

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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