[Bioperl-l] TreeIO for NHX format

Ameet Talwalkar ameet at eecs.berkeley.edu
Tue Oct 26 19:51:17 EDT 2010


Hi,

I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
format, and I have tried the following code:

*use Bio::TreeIO;

my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
                            -format => "phyloxml");
my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
                              -format => 'nhx');

while (my $tree = $input->next_tree) {
  $treeout->write_tree($tree);
}
*

The output is indeed in NHX format, but the tags (in particular I have a
duplication / speciation tag) does not appear in the output.  Am I doing
something wrong?

Thanks.

-Ameet


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