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 implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.FEEDBACK
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Reporting Bugs
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AUTHOR - Jason Stajich, Aaron Mackey, Justin Reese
Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.eduCONTRIBUTORS
Sendu Bala, [email protected]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 requirment
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).