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Two hundred replicate bootstrap datasets were generated and used for evaluation of parameter estimate precision.
Bootstrap datasets were generated using the SEQBOOT program from the PHYLIP package ver. 3.66 [104].
In our experiments, 100 bootstrap datasets were generated and ARACNe was used to generate a set of bootstrap networks.
For the final model, 500 bootstrap datasets were generated.
Parametric bootstrap datasets were generated using the parameter estimates from the illustrative datasets as parameter values.
Using the PHYLIP package, bootstrap datasets were generated with seqboot and used as input data for neighbor.
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To calculate a CIM-NPCI, B bootstrap datasets are generated and the peak of the LOD for each chromosome is calculated.
One hundred bootstrapped datasets were generated to obtain the mean and error on divergence time estimates for each dataset [ 40, 49].
For both the SMRs and the MLLC models, 200 bootstrapped datasets were generated and each was analysed in the same manner to determine 95% confidence intervals (CIs).
The pairwise Reynold's distances were computed using the Gendist program of the Phylip package [ 41] and 1,000 bootstrapped datasets were generated with Seqboot, followed by the Neighbor and Consense procedures from the same package to obtain a Neighbour-Joining consensus population tree.
34 First, 1,000 bootstrap replicate datasets were generated by using the program SeqBoot.
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