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

Heikki Lehvaslaiho heikki at ebi.ac.uk
Thu Apr 3 17:02:14 EST 2003


Your tree looks OK. I did not try to it with any program, so this is
just a wild guess, but try removing spaces from the tree and try again.

	-Heikki



On Thu, 2003-04-03 at 14:02, 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 objxect 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
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________



More information about the Bioperl-l mailing list