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

Jason Stajich jason.stajich at duke.edu
Fri Jul 1 14:48:26 EDT 2005

Can you send your code and an example file as a bug in http:// 

On Jun 30, 2005, at 12:55 PM, Georgii Bazykin wrote:

> Hi,
> 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!
> Yegor
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Jason Stajich
Duke University

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