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Actually, it's 24 million generations.
The analyses were run for one million generations for the bacterial dataset and 0.5 million generations for the eukaryotic dataset, sampled every 100 generations.
For each of the three setting, we performed 20 independent analyses of 20 million generations each, discarding the first 2 million generations of every replicate as burnin.
The first 4 million generations were discarded as burn-in, and a 50% majority rule consensus was constructed from the last one million generations (Fig. 3b).
The first 9 million generations were discarded as burnin, with a 50% majority rule consensus constructed from trees sampled from the last 1 million generations.
Following a pre-burnin of 1 million generations, both BEAST analyses were run for 10 million generations, sampling trees every 1000 generations.
To perform these calculations, we run BayesTraits for 100 million generations and applied a burn-in period of 10 million generations.
The analyses were performed with two independent chains and 20 million generations and chains were sampled every 1000 generations with a burn-in of 2 million generations.
Analyses were run for 50 million generations.
We conducted BEAST runs for 200 million generations with a burnin of 40 million generations.
The analysis was run twice, with 20 million generations per run (total 40 million generations).
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