beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
BEAST is usually deterministic, so starting with the same seed twice results in exactly the same output. Multi-threaded algorithms that use the `Randomizer` class in different threads does not show...
Hello! I am trying tu run BEAST2 on the command line and get an error that BEAST.base v2.7.6 is required but not installed. I tried to use the packagemanager to...
Hello, Thanks for developing this great software. I've been having a lot of trouble getting BEAST to work on my Mac (Ventura 13.5, M2 chip). When I try to run...
At the moment, it derives from Map, which derives from CalculationNode, but not from StateNode, making it cumbersome to do any operation on the Alignment during MCMC. Making Alignment a...
When installing a new package, currently any jar files in the lib directory remain there if not overwritten, and get loaded when BEAST, BEAUti etc start. This can cause problems...
Would it be possible to add partial monophyly constraints, that is, monophyly enforced only for a subset of taxa, while the rest are free to go anywhere in the tree?...
Dear @alexeid, please see below: ``` Starting frequencies: [0.25, 0.25, 0.25, 0.25] MultiGammaSiteModel is java-only -- unless you use MGSMBeagleTreeLikelihood UCRelaxedClockModel: using 1362 rate categories to approximate rate distribution across...
Methods like `Node.isDirectAncestor` and `Node.isFake` assume a tree in which branches of length 0 can occur, and this is an important case for me to include in a BEAST package...
Hi, I have a quick question as given in the title, prompted by the private getNr() function in the RandomLocalClockModel class which contains a conditional checking for a nodeNr greater...
