beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
Post processing programs that rely on multiple log files -- like Tracer for skyline analysis, or UglyTrees for visualising multi species coalescent trees -- rely on the log frequencies of...
Hello, I am new to BEAST, and was running an analysis on some 16 taxa of microalgae, and after running BEAST, I was feeding the resulting trees files into TreeAnnotate,...
The posterior of the testEBSP.xml fails for [TreePriorTest](https://github.com/CompEvol/beast2/blob/master/src/test/beast/beast2vs1/TreePriorTest.java). At some point it must have passed. When did this change and why? This might be a symptom of a bug introduced...
- Packagemanager command seems to work for installing packages. The packages visible in the file system at $BEAST_LIB packagemanager -add SSM -dir $BEAST_LIB - but after the package install, Packagemanager...
To reproduce: * Choose snapper template in BEAUti, and add `hemi129.nex` alignment. * In the priors panel, add MRCAPrior, there now is a choice of 4 taxa. * Go to...
Hi, I am learning BEAST2 these days. I figured out that the input genes has to be housekeeping gene. So I am trying to use all protein codeing gene in...
A sudden IndexError in an analysis had me stumped for some time. I have now figured out why it happens, but not how to fix it. Symptoms: For the analysis...
I am using command line TreeAnnotator on LogCombined tree files that range from size 3.2G to 12G. I keep getting the error message "java.lang.OutOfMemoryError: GC overhead limit exceeded" even when...
The trie in the `State` is a data structure that stores paths through the calculation graph based on which set of `StateNode`s are changed by operators. Some models have operators...
I have a BDSKY analysis with several Uniform MRCA priors with the tipsonly option set to true. When I try to resume the analysis I get -Inf for the first...
