IsLabelledNewick="true" or "false" ?

[walterxie]

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]

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

[walterxie]

CompEvol/beast2#1173

[walterxie]

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