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Bio::TreeIO::newick(3)User Contributed Perl DocumentatioBio::TreeIO::newick(3)

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

   print_tree_count
	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)

perl v5.14.1			  2011-07-22		Bio::TreeIO::newick(3)
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