NAME
Bio::NEXUS::Tree - provides a few functions for 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 : noneclone
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 : noneset_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 : noneset_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 : noneset_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 : noneis_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 : noneset_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 : noneis_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 : nonedetermine_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 : noneis_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 : noneas_string
Title : as_string
Usage : $treestring = $tree->as_string();
Function: Returns the tree as a string
Returns : tree string (string)
Args : noneas_string_inodes_nameless
Title : as_string_inodes_nameless
Usage : $treestring = $tree->as_string_inodes_nameless();
Function: Returns the tree as a string without internal node names
Returns : tree string (string)
Args : noneget_nodes
Title : get_nodes
Usage : @nodes = @{$tree->get_nodes()};
Function: Returns the list of ALL nodes in the tree
Returns : reference to array of nodes (Bio::NEXUS::Node objects)
Args : noneget_node_names
Title : get_node_names
Usage : @otu_names = @{$tree->get_node_names()};
Function: Returns the list of names of otus (terminal nodes)
Returns : array ref of node names
Args : noneget_distances
Title : get_distances
Usage : %distances = %{$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 : noneget_tree_length
Title : get_tree_length
Usage : $tre_length = $self->get_tree_length;
Function: Gets the total branch lengths in the tree.
Returns : total branch length
Args : noneget_support_values
Title : get_support_values
Usage : %bootstraps = %{$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 : noneset_depth
Title : set_depth
Usage : $tree->set_depth();
Function: Sets depth of root node
Returns : none
Args : noneget_depth
Title : get_depth
Usage : %depth=%{$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 : nonemax_depth
Title : max_depth
Usage : $maxdepth=%{$tree->max_depth()};
Function: Get maximum depth of tree
Returns : integer indicating maximum depth
Args : nonefind
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 objectreroot
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 outgroupselect_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 nameexclude_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