[BioRuby] newick to phyloxml
Christian M Zmasek
czmasek at burnham.org
Fri Jun 18 03:16:20 UTC 2010
Hi,
Unfortunately, this is not possible in a straightforward way.
The problem is that the tree object (Bio::Tree) returned by:
input = Bio::FlatFile.open(Bio::Newick, "tree.nh")
tree = input.next_entry.tree
is the parent type of the tree object(Bio::PhyloXML::Tree) required by:
writer = Bio::PhyloXML::Writer.new("tree.xml")
writer.write(phyloxml_tree)
Christian
K. Patil wrote:
> Hi,
>
> I noticed the inclusion of phyloxml support in bioruby, thanks a lot, its
> very useful. I was wondering if there is any straightforward way to
> convert a newick tree to phyloxml?
>
> best
>
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