# 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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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
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 (A:0.11,B:0.22):0.33; '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)
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)