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to ExaBayes
I'm attempting to run a 25 taxa, 193K bp dataset with 34 partitions, but I have been having issues with convergence in several parameters between runs, even after 10 million generations. I've set up the configuration file as follows:
and rediscovered the problem with the two likelihood peaks under ML.
So my suggestion is that you try re-analyzing the dataset with ML and
see if you get several peaks in the likelihood surface there as well to
be more confident that the dataset is difficult.