NAME

Bio::Phylo::Forest::NodeRole - Extra behaviours for a node in a phylogenetic tree

SYNOPSIS

 # some way to get nodes:
 use Bio::Phylo::IO;
 my $string = '((A,B),C);';
 my $forest = Bio::Phylo::IO->parse(
    -format => 'newick',
    -string => $string
 );

 # prints 'Bio::Phylo::Forest'
 print ref $forest;

 foreach my $tree ( @{ $forest->get_entities } ) {

    # prints 'Bio::Phylo::Forest::Tree'
    print ref $tree;

    foreach my $node ( @{ $tree->get_entities } ) {

       # prints 'Bio::Phylo::Forest::Node'
       print ref $node;

       # node has a parent, i.e. is not root
       if ( $node->get_parent ) {
          $node->set_branch_length(1);
       }

       # node is root
       else {
          $node->set_branch_length(0);
       }
    }
 }

DESCRIPTION

This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and recursion is possible, but there are also shrinkwrapped methods that return for example all terminal descendants of the focal node, or all internals, etc.

Node objects are inserted into tree objects, although technically the tree object is only a container holding all the nodes together. Unless there are orphans all nodes can be reached without recourse to the tree object.

METHODS

new()

Node constructor.

 Type    : Constructor
 Title   : new
 Usage   : my $node = Bio::Phylo::Forest::Node->new;
 Function: Instantiates a Bio::Phylo::Forest::Node object
 Returns : Bio::Phylo::Forest::Node
 Args    : All optional:
           -parent          => $parent,
           -taxon           => $taxon,
           -branch_length   => 0.423e+2,
           -first_daughter  => $f_daughter,
           -last_daughter   => $l_daughter,
           -next_sister     => $n_sister,
           -previous_sister => $p_sister,
           -name            => 'node_name',
           -desc            => 'this is a node',
           -score           => 0.98,
           -generic         => {
                -posterior => 0.98,
                -bootstrap => 0.80
           }

new_from_bioperl()

Node constructor from bioperl Bio::Tree::NodeI argument.

 Type    : Constructor
 Title   : new_from_bioperl
 Usage   : my $node =
           Bio::Phylo::Forest::Node->new_from_bioperl(
               $bpnode
           );
 Function: Instantiates a Bio::Phylo::Forest::Node object
           from a bioperl node object.
 Returns : Bio::Phylo::Forest::Node
 Args    : An objects that implements Bio::Tree::NodeI
 Notes   : The following BioPerl properties are copied:
           BioPerl output:        Bio::Phylo output:
           ------------------------------------------------
           id                     get_name
           branch_length          get_branch_length
           description            get_desc
           bootstrap              get_generic('bootstrap')
           
           In addition all BioPerl tags and values are copied
           to set_generic( 'tag' => 'value' );

prune_child()

Removes argument child node (and its descendants) from invocants children.

 Type    : Mutator
 Title   : prune_child
 Usage   : $parent->prune_child($child);
 Function: Removes $child (and its descendants) from $parent's children
 Returns : Modified object.
 Args    : A valid argument is Bio::Phylo::Forest::Node object.

collapse()

Collapse node.

 Type    : Mutator
 Title   : collapse
 Usage   : $node->collapse;
 Function: Attaches invocant's children to invocant's parent.
 Returns : Modified object.
 Args    : NONE
 Comments: If defined, adds invocant's branch 
           length to that of its children. If
           $node is in a tree, removes itself
           from that tree.

set_first_daughter()

Sets argument as invocant's first daughter.

 Type    : Mutator
 Title   : set_first_daughter
 Usage   : $node->set_first_daughter($f_daughter);
 Function: Assigns a node's leftmost daughter.
 Returns : Modified object.
 Args    : Undefines the first daughter if no
           argument given. A valid argument is
           a Bio::Phylo::Forest::Node object.

set_last_daughter()

Sets argument as invocant's last daughter.

 Type    : Mutator
 Title   : set_last_daughter
 Usage   : $node->set_last_daughter($l_daughter);
 Function: Assigns a node's rightmost daughter.
 Returns : Modified object.
 Args    : A valid argument consists of a
           Bio::Phylo::Forest::Node object. If
           no argument is given, the value is
           set to undefined.

set_previous_sister()

Sets argument as invocant's previous sister.

 Type    : Mutator
 Title   : set_previous_sister
 Usage   : $node->set_previous_sister($p_sister);
 Function: Assigns a node's previous sister (to the left).
 Returns : Modified object.
 Args    : A valid argument consists of
           a Bio::Phylo::Forest::Node object.
           If no argument is given, the value
           is set to undefined.

set_next_sister()

Sets argument as invocant's next sister.

 Type    : Mutator
 Title   : set_next_sister
 Usage   : $node->set_next_sister($n_sister);
 Function: Assigns or retrieves a node's
           next sister (to the right).
 Returns : Modified object.
 Args    : A valid argument consists of a
           Bio::Phylo::Forest::Node object.
           If no argument is given, the
           value is set to undefined.

set_node_below()

Sets new (unbranched) node below invocant.

 Type    : Mutator
 Title   : set_node_below
 Usage   : my $new_node = $node->set_node_below;
 Function: Creates a new node below $node
 Returns : New node if tree was modified, undef otherwise
 Args    : NONE

set_root_below()

Reroots below invocant.

 Type    : Mutator
 Title   : set_root_below
 Usage   : $node->set_root_below;
 Function: Creates a new tree root below $node
 Returns : New root if tree was modified, undef otherwise
 Args    : NONE
 Comments: This implementation is a port of @lh3's kn_reroot algorithm
           found here: http://lh3lh3.users.sourceforge.net/knhx.js

ACCESSORS

get_first_daughter()

Gets invocant's first daughter.

 Type    : Accessor
 Title   : get_first_daughter
 Usage   : my $f_daughter = $node->get_first_daughter;
 Function: Retrieves a node's leftmost daughter.
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_last_daughter()

Gets invocant's last daughter.

 Type    : Accessor
 Title   : get_last_daughter
 Usage   : my $l_daughter = $node->get_last_daughter;
 Function: Retrieves a node's rightmost daughter.
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_previous_sister()

Gets invocant's previous sister.

 Type    : Accessor
 Title   : get_previous_sister
 Usage   : my $p_sister = $node->get_previous_sister;
 Function: Retrieves a node's previous sister (to the left).
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_next_sister()

Gets invocant's next sister.

 Type    : Accessor
 Title   : get_next_sister
 Usage   : my $n_sister = $node->get_next_sister;
 Function: Retrieves a node's next sister (to the right).
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_ancestors()

Gets invocant's ancestors.

 Type    : Query
 Title   : get_ancestors
 Usage   : my @ancestors = @{ $node->get_ancestors };
 Function: Returns an array reference of ancestral nodes,
           ordered from young to old (i.e. $ancestors[-1] is root).
 Returns : Array reference of Bio::Phylo::Forest::Node
           objects.
 Args    : NONE

get_root()

Gets root relative to the invocant, i.e. by walking up the path of ancestors

 Type    : Query
 Title   : get_root
 Usage   : my $root = $node->get_root;
 Function: Gets root relative to the invocant
 Returns : Bio::Phylo::Forest::Node           
 Args    : NONE

get_farthest_node()

Gets node farthest away from the invocant. By default this is nodal distance, but when supplied an optional true argument it is based on patristic distance instead.

 Type    : Query
 Title   : get_farthest_node
 Usage   : my $farthest = $node->get_farthest_node;
 Function: Gets node farthest away from the invocant.
 Returns : Bio::Phylo::Forest::Node           
 Args    : Optional, TRUE value to use patristic instead of nodal distance

get_sisters()

Gets invocant's sisters.

 Type    : Query
 Title   : get_sisters
 Usage   : my @sisters = @{ $node->get_sisters };
 Function: Returns an array reference of sisters,
           ordered from left to right.
 Returns : Array reference of
           Bio::Phylo::Forest::Node objects.
 Args    : NONE

get_child()

Gets invocant's i'th child.

 Type    : Query
 Title   : get_child
 Usage   : my $child = $node->get_child($i);
 Function: Returns the child at index $i
 Returns : A Bio::Phylo::Forest::Node object.
 Args    : An index (integer) $i
 Comments: if no index is specified, first
           child is returned

get_descendants()

Gets invocant's descendants.

 Type    : Query
 Title   : get_descendants
 Usage   : my @descendants = @{ $node->get_descendants };
 Function: Returns an array reference of
           descendants, recursively ordered
           breadth first.
 Returns : Array reference of
           Bio::Phylo::Forest::Node objects.
 Args    : none.

get_terminals()

Gets invocant's terminal descendants.

 Type    : Query
 Title   : get_terminals
 Usage   : my @terminals = @{ $node->get_terminals };
 Function: Returns an array reference
           of terminal descendants.
 Returns : Array reference of
           Bio::Phylo::Forest::Node objects.
 Args    : NONE

get_internals()

Gets invocant's internal descendants.

 Type    : Query
 Title   : get_internals
 Usage   : my @internals = @{ $node->get_internals };
 Function: Returns an array reference
           of internal descendants.
 Returns : Array reference of
           Bio::Phylo::Forest::Node objects.
 Args    : NONE

get_mrca()

Gets invocant's most recent common ancestor shared with argument.

 Type    : Query
 Title   : get_mrca
 Usage   : my $mrca = $node->get_mrca($other_node);
 Function: Returns the most recent common ancestor
           of $node and $other_node.
 Returns : Bio::Phylo::Forest::Node
 Args    : A Bio::Phylo::Forest::Node
           object in the same tree.

get_leftmost_terminal()

Gets invocant's leftmost terminal descendant.

 Type    : Query
 Title   : get_leftmost_terminal
 Usage   : my $leftmost_terminal =
           $node->get_leftmost_terminal;
 Function: Returns the leftmost
           terminal descendant of $node.
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_rightmost_terminal()

Gets invocant's rightmost terminal descendant

 Type    : Query
 Title   : get_rightmost_terminal
 Usage   : my $rightmost_terminal =
           $node->get_rightmost_terminal;
 Function: Returns the rightmost
           terminal descendant of $node.
 Returns : Bio::Phylo::Forest::Node
 Args    : NONE

get_subtree()

Returns the tree subtended by the invocant

 Type    : Query
 Title   : get_subtree
 Usage   : my $tree = $node->get_subtree;
 Function: Returns the tree subtended by the invocant
 Returns : Bio::Phylo::Forest::Tree
 Args    : NONE

get_subtrees()

Returns the subtree rooted at the common ancestor of u and v, and the respective subtrees that contain u and v

 Type    : Query
 Title   : get_subtrees
 Usage   : my ( $found_u, $found_v, $subtree, $subtree_u, $subtree_v ) = $root->get_subtrees($u,$v);
 Function: Returns the tree subtended by the invocant
 Returns : A list containing the following variables:
           - boolean: did we find u
           - boolean: did we find v
           - Bio::Phylo::Forest::Node - the root node of the connecting subtree
           - Bio::Phylo::Forest::Node - the root node of the subtree for $u
           - Bio::Phylo::Forest::Node - the root node of the subtree for $v           
 Args    : Two nodes, $u and $v
 Comments: This is a recursive method that is used by the RANKPROB calculations (see 
           below). Typically you would invoke this method on the root node of the tree 
           containing $u and $v, and the method then recurses up the tree. The tree must 
           be bifurcating, or an exception is thrown.

TESTS

is_terminal()

Tests if invocant is a terminal node.

 Type    : Test
 Title   : is_terminal
 Usage   : if ( $node->is_terminal ) {
              # do something
           }
 Function: Returns true if node has
           no children (i.e. is terminal).
 Returns : BOOLEAN
 Args    : NONE

is_internal()

Tests if invocant is an internal node.

 Type    : Test
 Title   : is_internal
 Usage   : if ( $node->is_internal ) {
              # do something
           }
 Function: Returns true if node
           has children (i.e. is internal).
 Returns : BOOLEAN
 Args    : NONE

is_preterminal()

Tests if all direct descendents are terminal

 Type    : Test
 Title   : is_preterminal
 Usage   : if ( $node->is_preterminal ) {
              # do something
           }
 Function: Returns true if all direct descendents are terminal
 Returns : BOOLEAN
 Args    : NONE

is_first()

Tests if invocant is first sibling in left-to-right order.

 Type    : Test
 Title   : is_first
 Usage   : if ( $node->is_first ) {
              # do something
           }
 Function: Returns true if first sibling 
           in left-to-right order.
 Returns : BOOLEAN
 Args    : NONE

is_last()

Tests if invocant is last sibling in left-to-right order.

 Type    : Test
 Title   : is_last
 Usage   : if ( $node->is_last ) {
              # do something
           }
 Function: Returns true if last sibling 
           in left-to-right order.
 Returns : BOOLEAN
 Args    : NONE

is_root()

Tests if invocant is a root.

 Type    : Test
 Title   : is_root
 Usage   : if ( $node->is_root ) {
              # do something
           }
 Function: Returns true if node is a root       
 Returns : BOOLEAN
 Args    : NONE

is_descendant_of()

Tests if invocant is descendant of argument.

 Type    : Test
 Title   : is_descendant_of
 Usage   : if ( $node->is_descendant_of($grandparent) ) {
              # do something
           }
 Function: Returns true if the node is
           a descendant of the argument.
 Returns : BOOLEAN
 Args    : putative ancestor - a
           Bio::Phylo::Forest::Node object.

is_ancestor_of()

Tests if invocant is ancestor of argument.

 Type    : Test
 Title   : is_ancestor_of
 Usage   : if ( $node->is_ancestor_of($grandchild) ) {
              # do something
           }
 Function: Returns true if the node
           is an ancestor of the argument.
 Returns : BOOLEAN
 Args    : putative descendant - a
           Bio::Phylo::Forest::Node object.

is_sister_of()

Tests if invocant is sister of argument.

 Type    : Test
 Title   : is_sister_of
 Usage   : if ( $node->is_sister_of($sister) ) {
              # do something
           }
 Function: Returns true if the node is
           a sister of the argument.
 Returns : BOOLEAN
 Args    : putative sister - a
           Bio::Phylo::Forest::Node object.

is_child_of()

Tests if invocant is child of argument.

 Type    : Test
 Title   : is_child_of
 Usage   : if ( $node->is_child_of($parent) ) {
              # do something
           }
 Function: Returns true if the node is
           a child of the argument.
 Returns : BOOLEAN
 Args    : putative parent - a
           Bio::Phylo::Forest::Node object.

is_outgroup_of()

Test if invocant is outgroup of argument nodes.

 Type    : Test
 Title   : is_outgroup_of
 Usage   : if ( $node->is_outgroup_of(\@ingroup) ) {
              # do something
           }
 Function: Tests whether the set of
           \@ingroup is monophyletic
           with respect to the $node.
 Returns : BOOLEAN
 Args    : A reference to an array of
           Bio::Phylo::Forest::Node objects;
 Comments: This method is essentially the same as
           &Bio::Phylo::Forest::Tree::is_monophyletic.

can_contain()

Test if argument(s) can be a child/children of invocant.

 Type    : Test
 Title   : can_contain
 Usage   : if ( $parent->can_contain(@children) ) {
              # do something
           }
 Function: Test if arguments can be children of invocant.
 Returns : BOOLEAN
 Args    : An array of Bio::Phylo::Forest::Node objects;
 Comments: This method is an override of 
           Bio::Phylo::Listable::can_contain. Since node
           objects hold a list of their children, they
           inherit from the listable class and so they
           need to be able to validate the contents
           of that list before they are inserted.

CALCULATIONS

calc_path_to_root()

Calculates path to root.

 Type    : Calculation
 Title   : calc_path_to_root
 Usage   : my $path_to_root =
           $node->calc_path_to_root;
 Function: Returns the sum of branch
           lengths from $node to the root.
 Returns : FLOAT
 Args    : NONE

calc_nodes_to_root()

Calculates number of nodes to root.

 Type    : Calculation
 Title   : calc_nodes_to_root
 Usage   : my $nodes_to_root =
           $node->calc_nodes_to_root;
 Function: Returns the number of nodes
           from $node to the root.
 Returns : INT
 Args    : NONE

calc_max_nodes_to_tips()

Calculates maximum number of nodes to tips.

 Type    : Calculation
 Title   : calc_max_nodes_to_tips
 Usage   : my $max_nodes_to_tips =
           $node->calc_max_nodes_to_tips;
 Function: Returns the maximum number
           of nodes from $node to tips.
 Returns : INT
 Args    : NONE

calc_min_nodes_to_tips()

Calculates minimum number of nodes to tips.

 Type    : Calculation
 Title   : calc_min_nodes_to_tips
 Usage   : my $min_nodes_to_tips =
           $node->calc_min_nodes_to_tips;
 Function: Returns the minimum number of
           nodes from $node to tips.
 Returns : INT
 Args    : NONE

calc_max_path_to_tips()

Calculates longest path to tips.

 Type    : Calculation
 Title   : calc_max_path_to_tips
 Usage   : my $max_path_to_tips =
           $node->calc_max_path_to_tips;
 Function: Returns the path length from
           $node to the tallest tip.
 Returns : FLOAT
 Args    : NONE

calc_min_path_to_tips()

Calculates shortest path to tips.

 Type    : Calculation
 Title   : calc_min_path_to_tips
 Usage   : my $min_path_to_tips =
           $node->calc_min_path_to_tips;
 Function: Returns the path length from
           $node to the shortest tip.
 Returns : FLOAT
 Args    : NONE

calc_patristic_distance()

Calculates patristic distance between invocant and argument.

 Type    : Calculation
 Title   : calc_patristic_distance
 Usage   : my $patristic_distance =
           $node->calc_patristic_distance($other_node);
 Function: Returns the patristic distance
           between $node and $other_node.
 Returns : FLOAT
 Args    : Bio::Phylo::Forest::Node

calc_nodal_distance()

Calculates node distance between invocant and argument.

 Type    : Calculation
 Title   : calc_nodal_distance
 Usage   : my $nodal_distance =
           $node->calc_nodal_distance($other_node);
 Function: Returns the number of nodes
           between $node and $other_node.
 Returns : INT
 Args    : Bio::Phylo::Forest::Node

calc_terminals()

Calculates number of terminals subtended by the invocant

 Type    : Calculation
 Title   : calc_terminals
 Usage   : my $ntips = $node->calc_terminals;
 Function: Returns the number of terminals subtended by the invocant
 Returns : INT
 Args    : None

calc_rankprob_tipcounts()

Recurses from the root to the tips, returns an array reference at every step whose first element is a boolean set to true once the query node has been seen. The second element is an array that contains the number of subtended leaves - 1 for the query node and for all sisters of the nodes on the path from the query to the root. This method is used by the RANKPROB calculations (see below)

 Type    : Calculation
 Title   : calc_rankprob_tipcounts
 Usage   : my @rp = @{ $root->calc_rankprob_tipcounts($node) };
 Function: Returns tip counts for RANKPROB
 Returns : ARRAY
 Args    : NONE

calc_rankprob()

Calculates the probabilities for all rank orderings that the invocant node can occupy among all possible labeled histories. Uses Stadler's RANKPROB algorithm as described in:

Gernhard, T. et al., 2006. Estimating the relative order of speciation or coalescence events on a given phylogeny. Evolutionary Bioinformatics Online. 2:285. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674681/>.

 Type    : Calculation
 Title   : calc_rankprob
 Usage   : my @rp = @{ $root->calc_rankprob($node) };
 Function: Returns the rank probabilities of the invocant node
 Returns : ARRAY, indices are ranks, values are probabilities
 Args    : NONE

calc_expected_rank()

Calculates the expected rank and variance that the invocant node occupies among all possible labeled histories. Uses Stadler's RANKPROB algorithm as described in:

 Type    : Calculation
 Title   : calc_expected_rank
 Usage   : my ( $rank, $variance ) = $root->calc_expected_rank($node);
 Function: Calculates expected rank and variance
 Returns : Two numbers: rank and variance
 Args    : NONE

calc_rankprob_compare()

Calculates the probability that the argument node is below the invocant node over all possible labeled histories. Uses Stadler's COMPARE algorithm as described in:

 Type    : Calculation
 Title   : calc_rankprob_compare
 Usage   : my $prob = $root->calc_rankprob_compare($u,$v);
 Function: Compares rankings of nodes
 Returns : A number (probability)
 Args    : Bio::Phylo::Forest::Node

VISITOR METHODS

The methods below are similar in spirit to those by the same name in Bio::Phylo::Forest::Tree, except those in the tree class operate from the tree root, and those in this node class operate on an invocant node, and so these process a subtree.

visit_depth_first()

Visits nodes depth first

 Type    : Visitor method
 Title   : visit_depth_first
 Usage   : $tree->visit_depth_first( -pre => sub{ ... }, -post => sub { ... } );
 Function: Visits nodes in a depth first traversal, executes subs
 Returns : $tree
 Args    : Optional:
            # first event handler, is executed when node is reached in recursion
            -pre            => sub { print "pre: ",            shift->get_name, "\n" },
                        
            # is executed if node has a daughter, but before that daughter is processed
            -pre_daughter   => sub { print "pre_daughter: ",   shift->get_name, "\n" },
            
            # is executed if node has a daughter, after daughter has been processed 
            -post_daughter  => sub { print "post_daughter: ",  shift->get_name, "\n" },
            
            # is executed if node has no daughter
            -no_daughter    => sub { print "no_daughter: ",    shift->get_name, "\n" },                         

            # is executed whether or not node has sisters, if it does have sisters
            # they're processed first   
            -in             => sub { print "in: ",             shift->get_name, "\n" },

            # is executed if node has a sister, before sister is processed
            -pre_sister     => sub { print "pre_sister: ",     shift->get_name, "\n" }, 
            
            # is executed if node has a sister, after sister is processed
            -post_sister    => sub { print "post_sister: ",    shift->get_name, "\n" },         
            
            # is executed if node has no sister
            -no_sister      => sub { print "no_sister: ",      shift->get_name, "\n" }, 
            
            # is executed last          
            -post           => sub { print "post: ",           shift->get_name, "\n" },
            
            # specifies traversal order, default 'ltr' means first_daugher -> next_sister
            # traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
            -order          => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
            
            # passes sister node as second argument to pre_sister and post_sister subs,
            # and daughter node as second argument to pre_daughter and post_daughter subs
            -with_relatives => 1 # or any other true value
 Comments:

visit_breadth_first()

Visits nodes breadth first

 Type    : Visitor method
 Title   : visit_breadth_first
 Usage   : $tree->visit_breadth_first( -pre => sub{ ... }, -post => sub { ... } );
 Function: Visits nodes in a breadth first traversal, executes handlers
 Returns : $tree
 Args    : Optional handlers in the order in which they would be executed on an internal node:
                        
            # first event handler, is executed when node is reached in recursion
            -pre            => sub { print "pre: ",            shift->get_name, "\n" },
            
            # is executed if node has a sister, before sister is processed
            -pre_sister     => sub { print "pre_sister: ",     shift->get_name, "\n" }, 
            
            # is executed if node has a sister, after sister is processed
            -post_sister    => sub { print "post_sister: ",    shift->get_name, "\n" },         
            
            # is executed if node has no sister
            -no_sister      => sub { print "no_sister: ",      shift->get_name, "\n" },             
            
            # is executed whether or not node has sisters, if it does have sisters
            # they're processed first   
            -in             => sub { print "in: ",             shift->get_name, "\n" },         
            
            # is executed if node has a daughter, but before that daughter is processed
            -pre_daughter   => sub { print "pre_daughter: ",   shift->get_name, "\n" },
            
            # is executed if node has a daughter, after daughter has been processed 
            -post_daughter  => sub { print "post_daughter: ",  shift->get_name, "\n" },
            
            # is executed if node has no daughter
            -no_daughter    => sub { print "no_daughter: ",    shift->get_name, "\n" },                         
            
            # is executed last          
            -post           => sub { print "post: ",           shift->get_name, "\n" },
            
            # specifies traversal order, default 'ltr' means first_daugher -> next_sister
            # traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
            -order          => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
 Comments:

visit_level_order()

Visits nodes in a level order traversal.

 Type    : Visitor method
 Title   : visit_level_order
 Usage   : $tree->visit_level_order( sub{...} );
 Function: Visits nodes in a level order traversal, executes sub
 Returns : $tree
 Args    : A subroutine reference that operates on visited nodes.
 Comments:

SERIALIZERS

to_xml()

Serializes invocant to xml.

 Type    : Serializer
 Title   : to_xml
 Usage   : my $xml = $obj->to_xml;
 Function: Turns the invocant object (and its descendants )into an XML string.
 Returns : SCALAR
 Args    : NONE

to_newick()

Serializes subtree subtended by invocant to newick string.

 Type    : Serializer
 Title   : to_newick
 Usage   : my $newick = $obj->to_newick;
 Function: Turns the invocant object into a newick string.
 Returns : SCALAR
 Args    : takes same arguments as Bio::Phylo::Unparsers::Newick
 Comments: takes same arguments as Bio::Phylo::Unparsers::Newick

to_dom()

 Type    : Serializer
 Title   : to_dom
 Usage   : $node->to_dom($dom)
 Function: Generates an array of DOM elements from the invocant's
           descendants
 Returns : an array of Element objects
 Args    : DOM factory object

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. <http://dx.doi.org/10.1186/1471-2105-12-63>