Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface. # like from a TreeIO my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd'); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; my @leaves = $tree->get_leaves; This object holds handles to Taxonomic Nodes which make up a tree. use Bio::Species; use Bio::Taxonomy::Tree; my $human=new Bio::Species; my $chimp=new Bio::Species; my $bonobo=new Bio::Species; $human->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); $chimp->classification(qw( troglodytes Pan Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); $bonobo->classification(qw( paniscus Pan Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); # ranks passed to $taxonomy match ranks of species my @ranks = ('superkingdom','kingdom','phylum','subphylum', 'no rank 1','no rank 2','class','no rank 3','order', 'suborder','family','genus','species'); my $taxonomy=new Bio::Taxonomy(-ranks => \@ranks, -method => 'trust', -order => -1); my @nodes; my $tree1=new Bio::Taxonomy::Tree; my $tree2=new Bio::Taxonomy::Tree; push @nodes,$tree1->make_species_branch($human,$taxonomy); push @nodes,$tree2->make_species_branch($chimp,$taxonomy); my ($homo_sapiens)=$tree1->get_leaves; $tree1->splice($tree2); push @nodes,$tree1->add_species($bonobo,$taxonomy); my @taxa; foreach my $leaf ($tree1->get_leaves) { push @taxa,$leaf->taxon; } print join(", ",@taxa)."\n"; @taxa=(); $tree1->remove_branch($homo_sapiens); foreach my $leaf ($tree1->get_leaves) { push @taxa,$leaf->taxon; } print join(", ",@taxa)."\n"; See AUTHOR Email kortschak@rsbs.anu.edu.au Mainly Jason Stajich The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Taxonomy::Tree(); Function: Builds a new Bio::Taxonomy::Tree object Returns : Bio::Taxonomy::Tree Args :

get_nodes
Title : get_nodes Usage : my @nodes = $tree->get_nodes() Function: Return list of Bio::Taxonomy::Taxon objects Returns : array of Bio::Taxonomy::Taxon objects Args : (named values) hash with one value order => 'b|breadth' first order or 'd|depth' first order

get_root_node
Title : get_root_node Usage : my $node = $tree->get_root_node(); Function: Get the Top Node in the tree, in this implementation Trees only have one top node. Returns : Bio::Taxonomy::Taxon object Args : none

set_root_node
Title : set_root_node Usage : $tree->set_root_node($node) Function: Set the Root Node for the Tree Returns : Bio::Taxonomy::Taxon Args : Bio::Taxonomy::Taxon

get_leaves
Title : get_leaves Usage : my @nodes = $tree->get_leaves() Function: Return list of Bio::Taxonomy::Taxon objects Returns : array of Bio::Taxonomy::Taxon objects Args :

make_species_branch
Title : make_species_branch Usage : @nodes = $tree->make_species_branch($species,$taxonomy) Function: Return list of Bio::Taxonomy::Taxon objects based on a Bio::Species object Returns : array of Bio::Taxonomy::Taxon objects Args : Bio::Species and Bio::Taxonomy objects

make_branch
Title : make_branch Usage : $tree->make_branch($node) Function: Make a linear Bio::Taxonomy::Tree object from a leafish node Returns : Args : Bio::Taxonomy::Taxon object

splice
Title : splice Usage : @nodes = $tree->splice($tree) Function: Return a of Bio::Taxonomy::Tree object that is a fusion of two Returns : array of Bio::Taxonomy::Taxon added to tree Args : Bio::Taxonomy::Tree object

add_species
Title : add_species Usage : @nodes = $tree->add_species($species,$taxonomy) Function: Return a of Bio::Taxonomy::Tree object with a new species added Returns : array of Bio::Taxonomy::Taxon added to tree Args : Bio::Species object

add_branch
Title : add_branch Usage : $tree->add_branch($node,boolean) Function: Return a of Bio::Taxonomy::Tree object with a new branch added Returns : array of Bio::Taxonomy::Taxon objects of the resulting tree Args : Bio::Taxonomy::Taxon object boolean flag to force overwrite of descendent (see Bio::Node->add_Descendent)

remove_branch
Title : remove_branch Usage : $tree->remove_branch($node) Function: remove a branch up to the next multifurcation Returns : Args : Bio::Taxonomy::Taxon object