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We inferred each BES+ to be a unique region-derived sequence, and BES++ to be likely derived from repetitive sequences.
Based on the imputed HLA alleles, we inferred each individual's heterodimer type as one of DQ2.5 heterozygous, DQ2.5 homozygous, DQ2.2, or DQ8, according to the mapping in [ 8].
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Based on the loading of 7.5 Dox molecules per hybridized (TCG 8/ CGA 8 pair, and 72 copies of ONTs per NR, we inferred that each T-DNA-NR can load about 576 Dox molecules.
We inferred phylogenies for each sample with PHYML (version 2.4.4, [43]) using the F81 DNA substitution model, and plotted the resulting trees with the APE package (version 2.4, [44]) in R (version 2.10.0, [45], http://www.r-project.org).org
We inferred haplotypes for each individual based on the 5-marker haplotypes (rs17159772, rs4988494, rs2267721, rs4988498 and rs4988505) and compared the height of individuals that are likely (probability>0.5) to carry the negatively associated haplotype to that of non-carriers (Figure 3).
We inferred relationships in each population separately, since, according to Pemberton et al. (2010) there is no evidence for population-labeling errors.
In the synthetic analysis, we inferred networks for each experimental design and dataset and prior and sparsity level combination, which resulted in 1.7 million inferences (150 datasets × 5 priors × 6 accuracies × 381 sparsity levels).
We inferred divergence for each of five lineage-pairs by comparing across nucleotide divergence, previously estimated using population sequencing, and the coalescent model implemented in 3s that samples a single chromosome per locus.
Procedure (c) is applied to all leaf nodes until we inferred a model for each task.
We inferred substitution rates for each window as follows.
We inferred nuclear haplotypes for each locus (CHD1Z, MELK or Fib5) with DNASP v5.10 [ 58], using the data in subsequent analyses only if all sites had assignment probabilities ≥ 0.95.
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