[Bioperl-l] Bio::Taxonomy::Tree

[Rob Edwards]

One of your names contains parentheses:

Buchnera aphidicola str. APS (Acyrthosiphon pisum)

This was the only one I saw, but there could be others. Make sure that the 
names don't contain parentheses, commas, or semi-colons, as these have 
specific meanings in tree programs.

Rob


On Thursday 03 April 2003 07:02 am, Qiang Tu wrote:
> Hello all,
>
> I want to build a taxonomy tree of the complete genomes. In the program I
> built a Bio::Taxonomy::Taxon object at first, then use 'set_root_node'
> method to built a Bio::Taxonomy::Tree object by the taxon, then write the
> tree to a file by Bio::TreeIO object. The 'tabtree' method works, but the
> output files of 'newick' and 'nhx' methods can not be opened by other
> draw-tree software, such as treeview. The error message is: Extra pair of
> parentheses "()". The tree file is attached.
>
> Has anyone ever made such a taxonomy tree? Could you give me some samples
> so that I can find out the solution of my problem? Thanks.
>
> Qiang Tu
> Institute of Biochemistry and Cell Biology
> Chinese Academy of Sciences
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