[adegenet-forum] snapclust when HW is not expected

[brian knaus]

Hi and congrats on your snapclust paper! I was thinking of trying the
method on a couple of projects I'm working on. However, I work with fungi
and fungus-like plant pathogens that exhibit a mixture of reproductive
modes (e.g., selfing, clonality, mitotic reproduction). This means that we
do not necessarily expect Hardy-Weinberg assumptions to be met. Your manual
seems to come out pretty early stating that HW is important. I would guess
that linkage disequilibrium (non-independence of loci) may be an issue
also. So this raises my question: in systems where HW may not be assumed
and where there may be linkage disequilibrium would I be better of using
DAPC than snapclust?

Thanks!
Brian
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