Setting Nruns= and Nchains= for MrBayes on ABE
The reason for doing two "runs" is to see whether they obtain similar consensus trees and parameters. Making at least two runs is always recommended. The interface permits nruns=2 and nruns=4. Running odd numbers is inefficient AND slows your run down.
The MrBayes manual says: "By default, Nchains is set to 4, meaning that MrBayes will use 3 heated chains and one "cold" chain. In our experience, heating is essential for problems with more than about 50 taxa, whereas smaller problems often can be analyzed successfully without heating. Adding more than three heated chains may be helpful in analyzing large and difficult data sets."
Based on this information, we recommend that users set Nruns=2 and Nchains=4. Further, the interface currently limits nruns*nchains to be <= 16. nruns*nchains must be a multiple of 2.
If there is a tool or a feature you need, you can add it yourself or let us know.
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