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We also show the results we have obtained for tests from the CCP literature, the design of garbage collection zones, and salesmen areas distribution using the approach implemented for the SISROT® system.
The log2 intensity values were normalized using a loess transformation, and global dye and microarray effects were removed using the approach implemented Beehive.
To reveal those relationships that were consistently recovered by our analyses, we conducted rogue taxon filtering using the approach implemented in RogueNaRok (http://rnr.h-its.org/rnr, last accessed June 30 , 2014 (Aberer et al. 2013).
The trees were automatically rooted using the approach implemented in Phylogenie; taxonomic information for all sequences in each tree is used to put the root at the most-basal node that is most-distant from the sequence that was used to select the dataset [see Figure 4 in [ 83] for details].
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The ancestral sequences of whales were reconstructed using the Bayesian approach implemented in the BASEML program from the PAML package (Yang 2007).
The radiation hybrid analysis was performed for 1,171 molecular markers in total including previously published vectors of [ 18] using the TSP approach implemented in the rh_tsp_map2 software package in conjunction with the CONCORDE package [ 41].
Consequently, the silent site substitution rates in table 1 and figure 1 B were calculated using the ML approach, implemented through the program PAML v4 (Yang 2007).
Significance of FIS was tested by estimating the 95% confidence interval of the value for each population using the bootstrap approach implemented in Genetix (Belkhir et al. 2004).
The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY.
An in-depth phylogenetic analysis using more restricted sequence sampling representative (54 sequences, 187 positions, named BYKsel) of the diversity of BY-kinases was performed using the Bayesian approach implemented in MrBayes 3.2 program (Ronquist and Huelsenbeck 2003).
The phylogenetic analysis was performed using the Bayesian approach implemented in MrBayes version 3.2 [ 71].
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