Choosing Parameters for Jane

The parameters that have the most significant impact on the quality of the solution are Population Size and Number of Generations. Although the original Jane paper recommends having a population size twice that of the number of generations, our experience with larger trees (200+ nodes) has indicated that having the population size orders of magnitude larger than the number of generations is the best. For example, we have found that for 200 tip trees, the "sweet spot" seems to be a population of size 1300 with 30 generations. Users are encouraged to experiment with parameter values to see how they effect the quality of the solutions.

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