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  1. Tree painting should be inferred by the model

    Brownie and OUCH both take a "painted tree" to indicate which branches of the phylogeny operate under the same regime (assigned the same color). Different colors indicate different selective regimes. simmap can be used to infer possible paintings, (as can parsimony reconstruction), but it would be preferable to have the painting inferred as part of the model fitting of the OU models, directly from the data.

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      This is one of the primary goals of my thesis proposal. The full approach is outlined in the notebook, involving calculating the joint probability of the hybrid discrete-continuous model directly. Meanwhile, I’m attempting an inverse approach that generates a distribution of paintings first, then does the continuous inference.

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