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As explained in Section 4.4, SimAttack returns the most probable pair (query, user).
a) The most probable pair of haplotypes for each sample.
The final result is the most probable pair of alleles given the observed data at each locus.
We used PHASE v2.1.1 [ 34] to phase heterozygous sites within ITS, and retained the most probable pair of alleles for each heterozygous individual.
We have developed a new algorithm named PHLAT to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring.
We selected 15 SNPs with the strongest associations to either ear (p < 10−45) or body mass phenotypes (p < 10−15) and inferred haplotype patterns across these SNPs using the EM algorithm implemented in plink, assigning the most probable pair of haplotypes to each sample.
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To construct the alignment made by the MRF method (Bandyopadhyay et al., 2006), we downloaded the result file (http://www.cellcircuits.org/Bandyopadhyay2006/data/Bandyopadhyay_results.xls) with probabilities for all possible protein association, and we extracted the one-to-one alignment by taking the most probable pairs.
ProbKnot (Bellaousov and Mathews, 2010) assembles structures composed of the most probable base pairs from base-pairing probabilities that do not consider pseudoknots.
However, we also found that when the most probable haplotype pair has a probability between 0.3 and 0.7, the phase is likely to be incorrect.
Therefore, we separated the mixed signals only the most probable states pair [35] and, as indicated by the authors, this procedure achieves comparable scores to that of full estimation.
The most probable founder pair inferred by HAPPY agrees with our result at most sites.
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