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LinguaPhylo / LPhyBeast

Convert LPhy scripts to BEAST 2 XML
GNU Lesser General Public License v2.1
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IsLabelledNewick="true" or "false" ? #172

Open walterxie opened 1 week ago

walterxie commented 1 week ago

In TimeTreeToBEAST, should it uses IsLabelledNewick="true" or "false" as default:

BEAST 2 doc https://www.beast2.org/2014/07/28/all-about-starting-trees.html uses IsLabelledNewick="true", but this will cause the trouble when caring about the internal node index. Use "false", this problem will be solved.

alexeid commented 6 days ago

Surely false is wrong. Because in general we will not use only numbers for taxa names in lphy.

walterxie commented 4 days ago

https://github.com/CompEvol/beast2/issues/1173

walterxie commented 4 days ago

Yes, I think we should leave this unchanged and see how the above beast development will improve the internal node id issue ...