Provided by: libbio-perl-perl_1.7.2-2_all bug




         # 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;


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


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AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org


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

       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()

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

       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

       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)

       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
                  'traditional' --> draw bootstraps (100) like
       Returns : value of bootstrap_style (a scalar)
       Args    : on set, new value (a scalar or undef, optional)

       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)