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inCompEvol/BeastFX (press backspace or delete to remove)To replicate:
1. import Primates.nex alignment
2. link clock and trees
3. set firsthalf partition to HKY+4 gamma
4. clone firsthalf site model to second half site model There is an operator with id= ...
rbouckaert
- Opened on Oct 9, 2024
- #91
Hi, after the commit 917c22b I get an ant build error that complains about the static variables:
LogAnalyser.java:671: error: Illegal static declaration in inner class LogAnalyser.CoreRunnable
static ...
jugne
- 2
- Opened on Oct 7, 2024
- #90
When switching between tree prior subtemplates that use the same class, tree parameters are not updated correctly. This
is because members are added to beastfx.app.inputeditor.BeautiConfig.suppressBEASTObjects ...
- Opened on Sep 25, 2024
- #88
In NEXUS files, the trees come in the format tree STATE_ nr = (...); when produced by BEAST. It can be useful for
inspecting particular trees in a chain by this STATE_ nr information. Therefore, it is ...
- Opened on Sep 16, 2024
- #87
The -validate option for beast checks whether an XML file parses, but the MCMC class only performs its first likelihood
calculation when run() is called. Ideally, problems with initialisation and starting ...
- Opened on Sep 5, 2024
- #86
TreeAnnotator.MemoryFriendlyTreeSet is used in quite a few BEAST apps for post-processing trees, and is supposed to deal
with both NEXUS files containing trees and Newick tree sets. However, it fails to ...
- Opened on Jul 30, 2024
- #85
Hi Remco,
When instructing someone on the use of LogCombiner, I noticed that the resampling input field is confusingly labeled
Resample states at lower frequency .
From the label it s not clear exactly ...
tgvaughan
- 4
- Opened on Jul 10, 2024
- #84
When a partition name is the postfix of another partition name, and when linking the postfix is the name of the linked
partition it can happen that after unlinking the IDs of unlinked objects becomes mangled. ...
- Opened on Jun 24, 2024
- #83
Open any summarised tree created by TreeAnnotator, the tree ID is TREE1 . Instead, it will be nice to set it as the
method names, such as CCD0_CA.
taxa ...
;
tree TREE1 =...
End;
enhancement
walterxie
- Opened on Jun 10, 2024
- #82
Running loganalyser on trace files that are being written to can results in an out-of-bound exception when the file is
being written to between the time loganalyser determines how much memory to reserve ...
- Opened on Feb 4, 2024
- #81
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