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) ){ }
Describe the interface here
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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 _
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
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
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
Title : distance Usage : distance(-nodes => \@nodes ) Function: returns the distance between two given nodes Returns : numerical distance Args : -nodes => arrayref of nodes to test
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
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
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
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
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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.