[Biopython] Bug in Phylo.write('phyloxml')?

[Jon Sanders]

Archaeopteryx is the one program that read the trees fine. I also tried
HyperTree, TreeGraph2, and Treevolution, which failed.

-j

On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> My XML trees exported in biopython (with confidence values, thanks Eric!)
>> don't open in most XML tree viewing programs.
>>
>> The problem seems to be a spurious <name /> tag at the beginning of the
>> tree.
>>
>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>  <phy:phylogeny rooted="false">
>>    <phy:name />
>>    <phy:clade>
>>
>> If I delete this tag they open fine.
>>
>>
> Hi Jon,
>
> Thanks for reporting this. I'll check the spec to see if an empty 'name'
> tag is even valid. Can you give me the name of one or two programs that are
> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
> one of them?
>
> -Eric
>



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