NAME

       Bio::TreeIO::newick - parsing and writing of Newick/PHYLIP/New Hampshire 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://github.com/bioperl/bioperl-live/issues

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 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 : 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    : 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 Bio::Node::Node::each_Descendent() Returns : value of order_by (a scalar)
       Args    : on set, new value (a scalar or undef, optional)