Table 5

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

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


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.

Baele et al. BMC Evolutionary Biology 2011 11:145   doi:10.1186/1471-2148-11-145

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