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

[Qiang TU]

Hello,

Thank you all. Now I found the main problem is there are only one branch
at some level, which make too many brackets. For example,
(((a,b)),c);    does not work,
((a,b),c);       works.

I will try to find the solution. Thanks. :-)

Qiang Tu

---Original Message---
From: Rob Edwards<redwards at utmem.edu>
Subject: Re: [Bioperl-l] Bio::Taxonomy::Tree
 
>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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>

 
---End of Message---

 
Qiang Tu
Institute of Biochemistry and Cell Biology
Chinese Academy of Sciences
Email: tuqiang at mail.shcnc.ac.cn, tuqiang_cn at yahoo.com