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This causes problems for TreeAnnotator when annotating a tree with phylogeographical location information. TreeAnnotator uses TreeSetParser, which is marginally faster but uses a lot more memory. In l…
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For example:
```
$ treeannotator -burnin 10 -target
0 25 50 75 100
|--------------|--------------|--------------|--------------|
********************…
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Now that non-strict clocks are looking largely complete, the next major functionality hurdle is to add support for geography to BEASTling.
The plan is for this to be largely powered by yet more integ…
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If I parse this:
```
@InCollection{Madelung_1998_LB_10681727_56,
Title = {Cuprous oxide ({Cu$_2$O}) crystal structure, lattice parameters},
Author = {Madelung, O. and others},
Booktitle = {{L}a…
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I have come across several examples where specimens are linked as vouchers to publications, but these publications do not show up in the related projects that collected or used the specimen. Shouldn't…
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When running phylogeography:
"I get four trees all annotated slightly different when compared in a text editor. In SPREAD there are polygons for the B1TA1 tree, but not for the B1TA2 tree. Neither of…
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```
Hi Walter,
I think it's great that you've cleaned up the XML parser nomenclature for all
the different types of GeneralSubstitutionModel. So, let's keep that!
However, BEAST still needs to be…
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```
processValues[] in DiscreteTraitBranchRateModel should be size of the number of
states NOT the number of rates
double[] getProcessValues(final Tree tree, final NodeRef node)
```
Original issu…
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when saving, there is a light grey cross on the figure. If possible, it seems best to remove this
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It would be more consistent with the other analysis, and probably avoid user problems, if the posterior tree distribution needs to be loaded first (with its location attribute selection), and only the…