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We obtained REHH values using Sweep software v1.1 [ 35], (downloaded from http://www.broadinstitute.org/mpg/sweep).org/mpg/sweep
Analysis was carried out using Sweep software (Varilly P, Fry B, and Sabeti P, http://www.broadinstitute.org/mpg/sweep/).org/mpg/sweep/
The number of total and significant core haplotypes identified by the Sweep software was highest for the Italian Brown and lowest for the Piedmontese breed.
Haplotype bifurcation, EHH, and relative EHH (REHH) were analyzed using Sweep software v1.1 (Sabeti et al. 2002), which was downloaded from (http://www.broad.mit.edu/mpg/sweep).edu/mpg/sweep
In this LRH test, we assigned the core region containing four SNPs, rs77308790, rs6600143, rs2858925, and rs3760053, and the --SEA allele using the default parameters in the Sweep software (http://www.broadinstitute.org/mpg/sweep/).org/mpg/sweep/
We used the Sweep software [ 19] to analyze the haplotype structure in the genomic region encompassing EDAR; we selected a core containing the 370Ala/Val variant and used HapMap data from Asian individuals (Chinese and Japanese).
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That being said, it has not been a clean sweep against software patents, as the Federal Circuit has also upheld a patent claiming a method of creating a composite webpage using third-party product information within a host website.
Relative extended haplotype homozygosity (REHH) values were calculated using the Sweep 1.1 software (http://www.broadinstitute.org/mpg/sweep/).org/mpg/sweep/
The service model that has swept the software industry (business software anyway) means exactly that, customers need to be serviced (keep your mind out of the gutter) if they're going to remain customers.
For NewHybrids, we used the default genotype categories for first- and second-generations of crossing and ran 100,000 sweeps of five chains started from overdispersed starting values after a burn-in period of 50,000 sweeps following the software author's recommendation.
In addition to the above tests, we applied the approach of Galtier et al. implemented in the software SWEEP-BOTTLENECK [ 19] to detect significant traces of diversity reducing events, resulting from demographic (bottlenecks) or selective (sweeps) causes.
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