Bio::Tree::TreeFunctionsI(3)

NAME
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods

SYNOPSIS
  use Bio::TreeIO;
  my $in = new Bio::TreeIO(-format => 'newick', -file => 'tree.tre');

  my $tree = $in->next_tree;

  my @nodes = $tree->find_node('id1');

  if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){
   #...
  }

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

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich, Aaron Mackey, Justin Reese
Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.edu

CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk

Rerooting code was worked on by

  Daniel Barker d.barker-at-reading.ac.uk
  Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu

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

  find_node
 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
           OR
           -fieldname => $textstring

  remove_Node
 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

  get_lineage_nodes
 Title   : get_lineage_nodes
 Usage   : my @nodes = $tree->get_lineage_nodes($node);
 Function: Get the full lineage of a node (all its ancestors, in the order
           root->most recent ancestor)
 Returns : list of nodes
 Args    : either Bio::Tree::NodeI or string of the node id

  splice
 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
           -keep_*.
 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_*).

  get_lca
 Title   : get_lca
 Usage   : get_lca(-nodes => \@nodes ); OR
           get_lca(@nodes);
 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 commen ancestor
 Args    : -nodes => arrayref of nodes to test, OR
           just a list of nodes

  merge_lineage
 Title   : merge_lineage
 Usage   : merge_lineage($node)
 Function: Merge a lineage of nodes with this tree.
 Returns : n/a
 Args    : Bio::Tree::TreeI with only one leaf, OR
           Bio::Tree::NodeI which has an ancestor

 For example, if we are the tree $tree:

 +---B
 |
 A
 |
 +---C

 and we want to merge the lineage $other_tree:

 A---C---D

 After calling $tree->merge_lineage($other_tree), $tree looks like:

 +---B
 |
 A
 |
 +---C---D

  contract_linear_paths
 Title   : contract_linear_paths
 Usage   : contract_linear_paths()
 Function: Splices out all nodes in the tree that have an ancestor and only one
           descendent.
 Returns : n/a
 Args    : none

 For example, if we are the tree $tree:

             +---E
             |
 A---B---C---D
             |
             +---F

 After calling $tree->contract_linear_paths(), $tree looks like:

     +---E
     |
 A---D
     |
     +---F

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

  is_monophyletic
 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

  is_paraphyletic
 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

  reroot
 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

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