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https://github.com/CompEvol/beast2/blob/67dd40a56650490702f2616b56bcfc27a0b6e6fa/src/beast/base/evolution/tree/ClusterTree.java#L68
The "taxa" xml-input name confounds my user's eye since it takes …
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I created a new spacksite in **Myriad** using **Spack 0.22** on the `build01` node:
```shell
[ccspapp@build01 hpc-spack]$ spacksites/spacksites create fc-myriad-s0.22-test
/spack/0.22/fc-myria…
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```
2) The "Speciation: Birth-death serially sampled model", the ideal
parameterization would be (instead of bdss.birthRate, bdss.relativeDeathRate,
bdss.psi):
bdss.birthRate (=lambda keep as it is)…
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At the beginning of the run, BEAST2 shows:
java.lang.NullPointerException
at beast.evolution.likelihood.BeagleTreeLikelihood.setUpSubstModel(BeagleTreeLikelihood.java:474)
at beast.evolution.like…
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Hi all,
I'm using the beast2 package on a windows machine (windows 10), and after testing all beauti versions v.2.7.x, including under compatibility mode, none of them actually saves the xml file. …
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From Alexei:
We also need a unit test to check that unicode works for LPhyBEAST when it is not greek letters. I think currently it would fail. So we need to have a general approach to convert a unico…
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Hi,
I am trying to use CoupledMCMC for my mtDNA BEAST analysis - however, this package appears to have issues on my computer and I cannot figure out why. I was hoping you could offer me some advic…
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jblas doesn't support m1 (jblas-project/jblas#134 )as @tgvaughan mentioned in CompEvol/beast2#1047
This results in the following errror.
```
java.lang.reflect.InvocationTargetException
at jav…
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What is the reason that there are quite a few package-private (i.e. not marked as “private”, “protected” or “public”) fields in Beast2 classes?
I am now looking into writing a data type with appropri…
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I see this code in ClusterTree.java
``` java
public void initAndValidate() throws Exception {
if (Boolean.valueOf(System.getProperty("beast.resume")) &&
(isEstimatedInput.get() |…