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Table 5 Computational demands: number of iterations and computation time for the comparison of the different models in the thermodynamic integration framework.

From: Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes

Model Iterations System Time Time (corr.)
CP 1.020.000 4-core Opteron 7d 23 h -
CDCP 1.050.000 4-core Opteron 16d 7 h -
GY94 300.000 4-core Opteron 57d 21 h 203 days
GY94+Γ 150.000 8-core Xeon 29d 21 h 210 days
  1. The first column shows the type of model being considered: CP (codon partition), CDCP (context-dependent codon partition), with the most parameter-rich in each of these classes being chosen to provide the computational estimates. The second column contains the number of Bayesian MCMC iterations for the comparison of each class of models vis-à-vis the GTR model in the thermodynamic integration framework. Given the increased computational demands, fewer iterations were run for the GY94 model, which is reflected in the annealing and melting estimates being further apart (see Results section). The third column lists the computer architecture on which the calculations were run. The fourth column contains the computation time for the model comparisons if they would be executed on a single processor core. Finally, the fifth column provides an estimate of the computation time required for the GY94 model should an equal amount of iterations be run as for the CP and CDCP models.