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After 750,000 generations, trees were saved and 250 of them with standard deviation of split frequency < 0.01 were used later for the calculation of posterior probability.
After the burn-in, the effective sample sizes of all parameters were > 200, indicating that the analyses sampled the posterior distributions of each parameter satisfactorily, and the values of Average Standard Deviation of Split Frequency (ASDSF) were below 0.005.
Two separate runs of four Monte Carlo Markov chains (MCMC) (Yang and Rannala 1997) were run for 3,000,000 generations until the mean deviation of split frequency dropped below 0.01, and a tree was sampled every 1000th generation.
The response of the split frequency doublets and the circumstances under which travelling or standing wave responses, or a blend of the two, can occur in the structure's reference frame are also examined in the context of the model periodic structure.
Convergence of the parallel runs was confirmed by split frequency standard deviations (<0.001), and by potential scale reduction factors (PSRF; ∼1.0) for all model parameters.
The split frequency was below 0.01.
Similar(36)
The run was stopped when the standard deviation of split frequencies was below 0.01.
Convergence was assessed using the average standard deviation of split frequencies, output by MrBayes.
After all analyses, the average standard deviation of split frequencies was below 0.01.
The final average standard deviation of split frequencies at the end of the run was 0.036.
Additional generations were performed until the average standard deviation of split frequencies was less than 0.01.
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