Bio::Tree::TreeFunctionsI(3) Decorated Interface implementing basic Tree exploration methods


use Bio::TreeIO;
my $in = Bio::TreeIO->new(-format => 'newick', -file => 'tree.tre');
my $tree = $in->next_tree;
my @nodes = $tree->find_node('id1');
if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){


This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.


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AUTHOR - Jason Stajich, Aaron Mackey, Justin Reese

Email jason-at-bioperl-dot-org Email Email


Sendu Bala, [email protected]

Rerooting code was worked on by

  Daniel Barker
  Ramiro Barrantes


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


 Title   : find_node
 Usage   : my @nodes = $self->find_node(-id => 'node1');
 Function: returns all nodes that match a specific field, by default this
           is id, but different branch_length, 
 Returns : List of nodes which matched search
 Args    : text string to search for
           -fieldname => $textstring


 Title   : remove_Node
 Usage   : $tree->remove_Node($node)
 Function: Removes a node from the tree
 Returns : boolean represent status of success
 Args    : either Bio::Tree::NodeI or string of the node id


 Title   : get_lineage_nodes
 Usage   : my @nodes = $tree->get_lineage_nodes($node);
 Function: Given a node or its ID, get its full lineage, i.e. all its ancestors,
           from the root to the most recent ancestor. Only use the node ID as
           input if the nodes have been added to the tree.
 Returns : list of nodes
 Args    : either Bio::Tree::NodeI (or string of the node id)


 Title   : get_lineage_string
 Usage   : my $lineage = $tree->get_lineage_string($node);
 Function: Get the string representation of the full lineage of a node, e.g.
           for the Enterobacteriales node, return
           This method uses get_lineage_nodes internally and therefore inherits
           of all of its caveats.
 Returns : string
 Args    : * either Bio::Tree::NodeI (or string of the node id)
           * an optional separator (default: ';')


 Title   : splice
 Usage   : $tree->splice(-remove_id => \@ids);
 Function: Remove all the nodes from a tree that correspond to the supplied
           args, making all the descendents of a removed node the descendents
           of the removed node's ancestor.
           You can ask to explicitly remove certain nodes by using -remove_*,
           remove them conditionally by using -remove_* in combination with
           -keep_*, or remove everything except certain nodes by using only
 Returns : n/a
 Args    : just a list of Bio::Tree::NodeI objects to remove, OR
           -key => value pairs, where -key has the prefix 'remove' or 'keep',
           followed by an underscore, followed by a fieldname (like for the
           method find_node). Value should be a scalar or an array ref of
           scalars (again, like you might supply to find_node).
           So (-remove_id => [1, 2]) will remove all nodes from the tree that
           have an id() of '1' or '2', while
           (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with
           an id() of '1'.
           (-keep_id => [2]) will remove all nodes unless they have an id() of
           '2' (note, no -remove_*).
           -preserve_lengths => 1 : setting this argument will splice out
           intermediate nodes, preserving the original total length between
           the ancestor and the descendants of the spliced node. Undef 
           by default.


 Title   : get_lca
 Usage   : get_lca(-nodes => \@nodes ); OR
 Function: given two or more nodes, returns the lowest common ancestor (aka most
           recent common ancestor)
 Returns : node object or undef if there is no common ancestor
 Args    : -nodes => arrayref of nodes to test, OR
           just a list of nodes


 Title   : merge_lineage
 Usage   : merge_lineage($node)
 Function: Merge a lineage of nodes with this tree.
 Returns : true for success, false (and a warning) otherwise
 Args    : Bio::Tree::TreeI with only one leaf, OR
           Bio::Tree::NodeI which has an ancestor
 For example, if we are the tree $tree:
 and we want to merge the lineage $other_tree:
 After calling $tree->merge_lineage($other_tree), $tree looks like:


 Title   : contract_linear_paths
 Usage   : contract_linear_paths()
 Function: Splices out all nodes in the tree that have an ancestor and only one
 Returns : n/a
 Args    : none for normal behaviour, true to dis-regard the ancestor requirment
           and re-root the tree as necessary
 For example, if we are the tree $tree:
 After calling $tree->contract_linear_paths(), $tree looks like:
 Instead, $tree->contract_linear_paths(1) would have given:


  Example    : is_binary(); is_binary($node);
  Description: Finds if the tree or subtree defined by
               the internal node is a true binary tree
               without polytomies
  Returns    : boolean
  Exceptions : 
  Args       : Internal node Bio::Tree::NodeI, optional


 Title   : force_binary
 Usage   : force_binary()
 Function: Forces the tree into a binary tree, splitting branches arbitrarily
           and creating extra nodes as necessary, such that all nodes have
           exactly two or zero descendants.
 Returns : n/a
 Args    : none
 For example, if we are the tree $tree:
 (A has 6 descendants B-G)
 After calling $tree->force_binary(), $tree looks like:
     |   |
     |   +---X
 |   |
 |   |   +---G
 |   |   |
 |   +---X
 |       |
 |       +---F
 |       +---E
 |       |
 |   +---X
 |   |   |
 |   |   +---D
 |   |
     |   +---C
     |   |
 (Where X are artificially created nodes with ids 'artificial_n', where n is
 an integer making the id unique within the tree)


 Title   : simplify_to_leaves_string
 Usage   : my $leaves_string = $tree->simplify_to_leaves_string()
 Function: Creates a simple textual representation of the relationship between
           leaves in self. It forces the tree to be binary, so the result may
           not strictly correspond to the tree (if the tree wasn't binary), but
           will be as close as possible. The tree object is not altered. Only
           leaf node ids are output, in a newick-like format.
 Returns : string
 Args    : none


 Title   : distance
 Usage   : distance(-nodes => \@nodes )
 Function: returns the distance between two given nodes
 Returns : numerical distance
 Args    : -nodes => arrayref of nodes to test
           or ($node1, $node2)


 Title   : is_monophyletic
 Usage   : if( $tree->is_monophyletic(-nodes => \@nodes, 
                                      -outgroup => $outgroup)
 Function: Will do a test of monophyly for the nodes specified
           in comparison to a chosen outgroup
 Returns : boolean
 Args    : -nodes    => arrayref of nodes to test
           -outgroup => outgroup to serve as a reference


 Title   : is_paraphyletic
 Usage   : if( $tree->is_paraphyletic(-nodes =>\@nodes,
                                      -outgroup => $node) ){ }
 Function: Tests whether or not a given set of nodes are paraphyletic
           (representing the full clade) given an outgroup
 Returns : [-1,0,1] , -1 if the group is not monophyletic
                       0 if the group is not paraphyletic
                       1 if the group is paraphyletic
 Args    : -nodes => Array of Bio::Tree::NodeI objects which are in the tree
           -outgroup => a Bio::Tree::NodeI to compare the nodes to


 Title   : reroot
 Usage   : $tree->reroot($node);
 Function: Reroots a tree making a new node the root
 Returns : 1 on success, 0 on failure
 Args    : Bio::Tree::NodeI that is in the tree, but is not the current root


 Title   : reroot_at_midpoint
 Usage   : $tree->reroot_at_midpoint($node, $new_root_id);
 Function: Reroots a tree on a new node created halfway between the 
           argument and its ancestor
 Returns : the new midpoint Bio::Tree::NodeIon success, 0 on failure
 Args    : non-root Bio::Tree::NodeI currently in $tree
           scalar string, id for new node (optional)


 Title   : findnode_by_id
 Usage   : my $node = $tree->findnode_by_id($id);
 Function: Get a node by its id (which should be 
           unique for the tree)
 Returns : L<Bio::Tree::NodeI>
 Args    : node id


 Title   : move_id_to_bootstrap
 Usage   : $tree->move_id_to_bootstrap
 Function: Move internal IDs to bootstrap slot
 Returns : undef
 Args    : undef


 Title   : add_trait
 Usage   : my $key = $tree->add_trait($trait_file, 3);
 Function: Add traits to the leaf nodes of a Bio::Tree:Tree from a file.
           The trait file is a tab-delimited text file and needs to have a
           header line giving names to traits. The first column contains the
           leaf node ids. Subsequent columns contain different trait value sets.
           Single or double quotes are removed from the trait values. Traits
           are added to leaf nodes as a tag named $key using the add_tag_value()
           method. This means that you can retrieve the trait values using the
           get_tag_values() method (see the documentation for Bio::Tree::Node).
 Returns : Trait name (a scalar) on success, undef on failure (for example, if
           the column index requested was too large).
 Args    : * Name of trait file (scalar string).
           * Index of trait file column (scalar int). Note that numbering starts
             at 0. Default: 1 (second column).
           * Ignore missing values. Typically, if a leaf node has no value in
             the trait file, an exception is thrown. If you set this option to
             1, then no trait will be given to the node (no exception thrown).