[Bioperl-l] TreeIO::nhx doesn't write internal node labels

Georgii Bazykin gbazykin at Princeton.EDU
Thu Jun 30 12:55:56 EDT 2005


I am new to BioPerl, and I am having trouble trying to save a tree in
NHX format. I load a nexus tree and parse a PAUP log file ("branch
linkages") to get internal node ids (I will then need to process
character changes between internal nodes, this is why I need internal
node ids). I then put write PAUP ids (which are numbers) as ids of
internal nodes of the tree, and write the tree in nxh format, hoping
that the internal node labels will be preserved. But the resulting nhx
file has only empty [&&NHX] labels and no internal node labels. Is
this a feature, or am I doing something wrong?

Please help!


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