[Biopython-dev] [Fwd: Bug in Biopython Phyloxml reader]

Brad Chapman chapmanb at 50mail.com
Wed Jun 15 13:03:54 UTC 2011

Thanks for reporting the problem. The Biopython mailing lists
(http://biopython.org/wiki/Mailing_lists) are the right place to
report these types of issues.

Hopefully Eric or someone else on the list will be able to help.
Thanks again,

----- Forwarded message from Nicolas Rochette <nicolas.rochette at univ-lyon1.fr> -----

Date: Wed, 15 Jun 2011 14:25:09 +0200


I apologize for contacting you directly, but I could not find the
right place for this report. Could you please forward it ?

The bug is about 0-length terminal branches being given a length of 1
; please find an example below.


Nicolas Rochette
PhD student
Laboratory for Biometry and Evolutive Biology
Lyon, France


echo '(A:2,(B:0,C:3):0,D:5);' > foo.newick
java -cp forester.jar org.forester.application.phyloxml_converter
-f=nn -i foo.newick foo.phyloxml
python -c 'from Bio import Phylo;
Phylo.write(Phylo.read("foo.phyloxml","phyloxml"), "bar.newick",
cat bar.newick


----- End forwarded message -----

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