/ 
bioperl-1.2.3
/ Bio::Tree::TreeFunctionsI

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(-clade => @nodes, -outgroup => $outnode) ){

}

DESCRIPTION

Describe the interface here

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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.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

Additional contributors names and emails here

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_lca

Title   : get_lca
Usage   : get_lca(-nodes => \@nodes )
Function: given two nodes, returns the lowest common ancestor
Returns : node object
Args    : -nodes => arrayref of nodes to test

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_tree
Usage   : $tree->reroot($node);
Function: Reroots a tree either 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

reverse_edge

Title   : reverse_edge
Usage   : $node->reverse_edge(child);
Function: makes child be a parent of node
Requires: child must be a direct descendent of node
Returns : nothing
Args    : Bio::Tree::NodeI that is in the tree

delete_edge

Title   : delete_edge
Usage   : $node->reverse_edge(child); 
Function: makes child be a parent of node
Requires: child must be a direct descendent of node
Returns : nothing
Args    : Bio::Tree::NodeI that is in the tree