Bio::Tree::TreeFunctionsI(3pm)

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

SYNOPSIS
  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) ){
   #...
  }

DESCRIPTION
This interface provides a set of implemented 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

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  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:

  https://github.com/bioperl/bioperl-live/issues

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: 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)

  get_lineage_string
 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
           Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales.
           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: ';')

  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_*).

           -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.

  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 common 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 : 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:

 +---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 normal behaviour, true to dis-regard the ancestor requirement
           and re-root the tree as necessary

 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

 Instead, $tree->contract_linear_paths(1) would have given:

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

  is_binary
  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

  force_binary
 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:

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

 (A has 6 descendants B-G)

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

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

 (Where X are artificially created nodes with ids 'artificial_n', where n is
 an integer making the id unique within the tree)

  simplify_to_leaves_string
 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

  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
           or ($node1, $node2)

  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

  reroot_at_midpoint
 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)

  findnode_by_id
 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

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

  add_trait
 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).