Then an attenuation map was generated using the algorithm implemented in the scanner software, assuming the tissue attenuation coefficient value to be uniform [9].
Recombination rates were inferred directly from sequence data using the algorithm implemented in LDhat [48].
For this experiment, we decided to use a random forests algorithm (RF) as a base classifier (we are using the algorithm implemented in [3] for reproducibility purposes), generating 150 trees.
Multi-class significance analysis (SAM) was done using the algorithm implemented in MeV from TM4 software.
PCA was performed using the algorithm implemented in MATLAB, R2009b (MathWorks, Natick, MA, USA).
Data were analyzed, using the algorithm implemented in the statistical package qpcR (version 1.3-6) (Ritz and Spiess 2008).
The most straightforward application of AGE is single-nucleotide SV breakpoint resolution and standardization, as has just been demonstrated by using the algorithm implemented in AGE software.
Linkage disequilibrium simulations were carried out by the WH program [ 51, 52] and Markov Chain Monte Carlo (MCMC) simulations of the isolation with migration model were performed using the algorithm implemented in the IM program [ 39].
The tree was constructed using the algorithm implemented in PhyML version 3.0.1, 4 and the model of sequence evolution used was the generalized time-reversible (GTR) model with γ-distributed rate variation.
Using the algorithm implemented into the program BEAGLE, we haplotyped the 75 animals of the complex pedigree in Figure 1 with 1 976 SNP on BTA5 that are informative in the Fleckvieh population.
