Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods 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) ){ } This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.

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/ Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.edu 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 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