To measure the extent of linkage disequilibrium between any pairwise markers, we first inferred phase and reconstructed haplotypes using the PHASE software (http://www.stat.washington. edu/stephens/phase.html) developed by Stephens et al, 2001).
According to different SNPs, the paternal and maternal haplotypes were determined by phase software.
During the implementation phase software bugs are introduced, some of which can be exploited to break the system and extract private information.
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure.
At the design phase, software is constantly in adaptation by the building process itself, and at runtime, it can be adapted in response to changing conditions in the executing environment such as location or resources.
Genotype consistent HLA haplotypes for the BMDR data were constructed with the PHASE software [16].
Then, we used the PHASE software (http://www.bioinf.manchester.ac.uk/resources/phase) providing such partitioned models and performing Bayesian phylogenetic inferences [67].
Phase software was used to reconstruct haplotypes to include the SNPs not present in the HapMap data [17].
We use the MCMC-based PHASE software [30] to draw from π(HF) samples of HF, denoted HF(1), HF(2),.., HF M).
Haplotypes were first estimated using the PHASE software [54], and then computed by logistic analyses using the Statistical Analysis System (SAS) program.
For the same reason, we did not explicitly account in our modeling for the uncertainties in the reconstruction of haplotypes from the BMDR data [26], although such measures would have been available from the output of the PHASE software.
