Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::Tree

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NAME ^

Bio::NEXUS::Tree - Provides functions for manipulating trees

SYNOPSIS ^

new Bio::NEXUS::Tree;

DESCRIPTION ^

Provides a few useful functions for trees.

FEEDBACK ^

All feedback (bugs, feature enhancements, etc.) are all greatly appreciated. There are no mailing lists at this time for the Bio::NEXUS::Tree module, so send all relevant contributions to Dr. Weigang Qiu (weigang@genectr.hunter.cuny.edu).

AUTHORS ^

 Eugene Melamud (melamud@carb.nist.gov)
 Thomas Hladish (tjhladish at yahoo)
 Weigang Qiu (weigang@genectr.hunter.cuny.edu)
 Chengzhi Liang (liangc@umbi.umd.edu)
 Peter Yang (pyang@rice.edu)

METHODS ^

new

 Title   : new
 Usage   : $tree = new Bio::NEXUS::Tree();
 Function: Creates a new Bio::NEXUS::Tree object
 Returns : Bio::NEXUS::Tree object
 Args    : none

clone

 Name    : clone
 Usage   : my $new_tree = $self->clone();
 Function: clone a Bio::NEXUS::Tree (self) object. All the nodes are also cloned. 
 Returns : new Bio::NEXUS::Tree object
 Args    : none

set_rootnode

 Title   : set_rootnode
 Usage   : $tree->set_rootnode($newnode);
 Function: Sets the root node to a new node
 Returns : none
 Args    : root node (Bio::NEXUS::Node object)

get_rootnode

 Title   : get_rootnode
 Usage   : $node = $tree->get_rootnode();
 Function: Returns the tree root node 
 Returns : root node (Bio::NEXUS::Node object)
 Args    : none

set_name

 Title   : set_name
 Usage   : $tree->set_name($name);
 Function: Sets the tree name
 Returns : none
 Args    : name (string)

get_name

 Title   : get_name
 Usage   : $name = $tree->get_name();
 Function: Returns the tree's name
 Returns : name (string) or undef if name doesn't exist
 Args    : none

set_as_default

 Title   : set_as_default
 Usage   : $tree->set_as_default();
 Function: assigns is_default variable for this object to 1. (default : 0)
 Returns : none
 Args    : none

is_default

 Title   : is_default
 Usage   : $is_default_tree = $tree->is_default();
 Function: check whether the tree is assigned as the default.
 Returns : 0 (false) or 1 (true)
 Args    : none

set_as_unrooted

 Title   : set_as_unrooted
 Usage   : $tree->set_as_unrooted();
 Function: assigns is_unrooted variable for this object to 1. (default : 0)
 Returns : none
 Args    : none

is_rooted

 Title   : is_rooted
 Usage   : $is_rooted_tree = $tree->is_rooted();
 Function: Check whether the tree is rooted.
 Returns : 0 (false) or 1 (true)
 Args    : none

determine_cladogram

 Title   : determine_cladogram
 Usage   : $tree->determine_cladogram();
 Function: Determine if a tree is a cladogram or not (that is, whether branch lengths are present)
 Returns : none
 Args    : none

set_output_format

 Title   : set_output_format 
 Usage   : $tree->set_output_format('STD');  
 Function: Sets the output format for the Tree, (options : STD or NHX)
 Returns : none
 Args    : string: 'STD' or 'NHX'

get_output_format

 Title   : get_output_format 
 Usage   : $output_format = $tree->get_output_format();  
 Function: Returns the output format for the Tree, (options : STD or NHX)
 Returns : string: 'STD' or 'NHX'
 Args    : none

is_cladogram

 Title   : is_cladogram
 Usage   : &dothis() if $tree->is_cladogram();
 Function: Returns whether tree is a cladogram or not
 Returns : 0 (no) or 1 (yes)
 Args    : none

as_string

 Title   : as_string
 Usage   : $treestring = $tree->as_string();
 Function: Returns the tree as a string
 Returns : tree string (string)
 Args    : none

as_string_inodes_nameless

 Title   : as_string_inodes_nameless
 Usage   : $treestring = $tree->as_string_inodes_nameless();
 Function: Returns the tree as a string without internal node names
 Returns : tree string (string)
 Args    : none

get_nodes

 Title   : get_nodes
 Usage   : @nodes = @{$tree->get_nodes()};
 Function: Returns the list of ALL nodes in the tree
 Returns : reference to array of nodes (Bio::NEXUS::Node objects)
 Args    : none

get_node_names

 Title   : get_node_names
 Usage   : @otu_names = @{$tree->get_node_names()};
 Function: Returns the list of names of otus (terminal nodes)
 Returns : array ref of node names
 Args    : none

get_distances

 Title   : get_distances
 Usage   : %distances = %{$tree->get_distances()};
 Function: Finds the distances from the root node for all OTUs
 Returns : reference to a hash of OTU names as keys and distances as values
 Args    : none

get_tree_length

 Title   : get_tree_length
 Usage   : $tre_length  = $self->get_tree_length;
 Function: Gets the total branch lengths in the tree.
 Returns : total branch length
 Args    : none

get_support_values

 Title   : get_support_values
 Usage   : %bootstraps = %{$tree->get_support_values()};
 Function: Finds all branch support values for all OTUs
 Returns : reference to a hash where OTU names are keys and branch support values are values
 Args    : none

set_depth

 Title   : set_depth
 Usage   : $tree->set_depth();
 Function: Sets depth of root node
 Returns : none
 Args    : none

get_depth

 Title   : get_depth
 Usage   : %depth=%{$tree->get_depth()};
 Function: Get depth in tree of all OTUs and internal nodes
 Returns : reference to hash with keys = node names and values = depth
 Args    : none

max_depth

 Title   : max_depth
 Usage   : $maxdepth=%{$tree->max_depth()};
 Function: Get maximum depth of tree
 Returns : integer indicating maximum depth
 Args    : none

find

 Title   : find
 Usage   : $node = $tree->find($name);
 Function: Finds the first occurrence of a node called 'name' in the tree
 Returns : Bio::NEXUS::Node object
 Args    : name (string)

find_all

 Title   : find_all
 Usage   : @nodes = @{ $tree->find_all($name) };
 Function: find all occurrences of nodes called 'name' in the tree
 Returns : Bio::NEXUS::Node objects
 Args    : name (string)

prune

 Name    : prune
 Usage   : $tree->prune($OTUlist);
 Function: Removes everything from the tree except for OTUs specified in $OTUlist
 Returns : none
 Args    : list of OTUs (string)

equals

 Name    : equals
 Usage   : $tree->equals($another_tree);
 Function: compare if two trees are equivalent in topology
 Returns : 1 if equal or 0 if not
 Args    : another Bio::NEXUS::Tree object

reroot

 Name    : reroot
 Usage   : $tree = $tree->reroot($outgroup_name);
 Function: re-root a tree with a node as outgroup
 Returns : 
 Args    : the node name to be used as new outgroup

select_subtree

 Name    : select_subtree
 Usage   : $new_tree_obj = $self->select_subtree($node_name);
 Function: selects the subtree (the given node and all its children) from the tree object.
 Returns : new Bio::NEXUS::Tree object
 Args    : Node name

exclude_subtree

 Name    : exclude_subtree
 Usage   : $new_tree_obj = $self->exclude_subtree($node_name);
 Function: removes the given node and all its children from the tree object.
 Returns : new Bio::NEXUS::Tree object
 Args    : Node name

get_mrca_of_otus

 Name    : get_mrca_of_otus
 Usage   : $node = $self->get_mrca_of_otus($otus);
 Function: gets the most recent common ancestor for the input $otus
 Returns : Bio::NEXUS::Node object
 Args    : $otus : Array reference of the OTUs
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