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The BOP method is implemented with the program OptMapsIS.
The hierarchical models were implemented with the program WinBUGS 1.4.3 [ 16].
BI was implemented with the program Mr.Bayes v3.1.2 [ 59] under a partitioned model (dataset divided into genes), and considering the model of nucleotide substitution estimated with jModelTest.
Lennard-Jones parameters 12-10 and 12-6, implemented with the program, were used for modeling H-bonds and van der Waals interactions, respectively.
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Finally, Section 4.4 describes a set of data analysis case studies that have been implemented with the programming languages discussed in the previous sections.
Then we review the Meta-learning algorithm and propose our framework MMR which is implemented with the programming model of MapReduce on Hadoop.
It should be emphasized that most of these functional predictions or annotations are based on weak similarity to conserved domains (CD) as identified by the CD search program implemented with the BLAST program [ 47].
Such integration is based on 'certainty factors', and is implemented with the computer program BMP90 with a global inference engine.
Bayesian methods implemented with the computer program MrBayes v3.1.1 [32], [32] were applied to generate the dendrograms and to assess statistical supports for the branches from 16,000 trees generated from the original dataset.
Heuristic parsimony analyses were implemented with the computer program PAUP*4.0b10.
The representation of the electrostatic potentials in the modeled 3D structures was implemented with the VMD program [ 59].
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