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Uncertain diploid sequences were phased computationally using PHASE version 2.1 [ 35] with five replicate runs of a 2,000 step Markov chain, a burn-in of 1,000 steps, and a thinning interval of 2. We were able to phase 43 individuals computationally using an output probability threshold of 95%.
The diploid sequences were phased into haplotypes using PHASE version 2.1 with default parameters (Stephens and Donnelly 2003; Stephens et al. 2001).
Imputation and phasing were performed simultaneously with the PHASE version 2.1 software package (Stephens et al. 2001) but in two separate groups for the HGDP and SAC/Peru populations because the groups were missing different sets of three SNPs.
Haplotype phase of nuclear genes was determined using PHASE version 2.1.1.
After sequencing, the haplotypic phases of the introns were determined using PHASE version 2.1.1 [ 47], with a threshold of 0.9.
Phased haplotypes and missing data were inferred using PHASE (version 2.1) (45, 45).
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The two-phase version (V2) works much better than the direct (V1) version in all cases.
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From the parametric study (Fig. 15), the following remarks can be made: The two-phase version (V2) works much better than the direct (V1) version in all cases.
A simple two-phase version of the κ-ϵ turbulence model has been applied to describe the hydrodynamics of a vertical riser reactor.
An enhanced single-phase version of INSENS scales to large networks, integrates bidirectional verification to defend against rushing attacks, accommodates multipath routing to multiple base stations, enables secure joining/leaving, and incorporates a novel pairwise key setup scheme based on transitory global keys that is more resilient than LEAP.
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