= Phase averaging in a linkage likelihood
{title2=$L(\theta)=\sum_s\pi_sL_s(\theta)$}
An unphased multilocus <genotype> can have several pairs of <haplotypes>. Its <pedigree likelihood> must average over these possible phases with prior weights $\pi_s$, rather than maximize over phases after observing the offspring. Under <linkage disequilibrium>, the weights need not be equal. They can be obtained by conditioning population haplotype frequencies on the observed parental <genotype>; different choices of what is conditioned on change only parameter-independent factors when those frequencies are held fixed.
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