[BioRuby] newick to phyloxml

Christian M Zmasek czmasek at burnham.org
Thu Jun 17 23:16:20 EDT 2010


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")


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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