Bio::TreeIO::newick.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::TreeIO::newick - TreeIO implementation for parsing
  Newick/New Hampshire/PHYLIP format.

SYNOPSIS

   # do not use this module directly
   use Bio::TreeIO;
   my $treeio = Bio::TreeIO->new(-format => 'newick', 
                                -file => 't/data/LOAD_Ccd1.dnd');
   my $tree = $treeio->next_tree;
 
 

DESCRIPTION

This module handles parsing and writing of Newick/PHYLIP/New Hampshire format.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Args    : -print_count     => boolean  default is false
            -bootstrap_style => set the bootstrap style (one of nobranchlength,
                                                         molphy, traditional)
            -order_by        => set the order by sort method 
                                (see L<Bio::Node::Node::each_Descendent()> )
 
 

next_tree

  Title   : next_tree
  Usage   : my $tree = $treeio->next_tree
  Function: Gets the next tree in the stream
  Returns : L<Bio::Tree::TreeI>
  Args    : none
 
 

write_tree

  Title   : write_tree
  Usage   : $treeio->write_tree($tree);
  Function: Write a tree out to data stream in newick/phylip format
  Returns : none
  Args    : L<Bio::Tree::TreeI> object
 
 
  Title   : print_tree_count
  Usage   : $obj->print_tree_count($newval)
  Function: Get/Set flag for printing out the tree count (paml,protml way)
  Returns : value of print_tree_count (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

bootstrap_style

  Title   : bootstrap_style
  Usage   : $obj->bootstrap_style($newval)
  Function: A description of how bootstraps and branch lengths are
            written, as the ID part of the internal node or else in []
            in the branch length (Molphy-like; I am sure there is a
            better name for this but am not sure where to go for some
            sort of format documentation)
 
            If no branch lengths are requested then no bootstraps are usually
            written (unless someone REALLY wants this functionality...)
 
            Can take on strings which contain the possible values of
            'nobranchlength'   --> don't draw any branch lengths - this
                                   is helpful if you don't want to have to 
                                   go through and delete branch len on all nodes
            'molphy' --> draw bootstraps (100) like
                                   (A:0.11,B:0.22):0.33[100];
            'traditional' --> draw bootstraps (100) like
                                   (A:0.11,B:0.22)100:0.33;
  Returns : value of bootstrap_style (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

order_by

  Title   : order_by
  Usage   : $obj->order_by($newval)
  Function: Allow node order to be specified (typically "alpha")
            See L<Bio::Node::Node::each_Descendent()>
  Returns : value of order_by (a scalar)
  Args    : on set, new value (a scalar or undef, optional)