Bio::TreeIO::newick(3pm) User Contributed Perl Documentation Bio::TreeIO::newick(3pm)
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:
https://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::TreeIO::newick(3pm)