Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
# get a Bio::Tree::TreeI somehow # 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;
This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI.
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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://bioperl.org/bioperl-bugs/
Email jason@bioperl.org
Elia Stupka, elia@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_nodes Usage : my @nodes = $tree->get_nodes() Function: Return list of Tree::NodeI objects Returns : array of Tree::NodeI objects Args : (named values) hash with one value order => 'b|breadth' first order or 'd|depth' first order
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::Tree::NodeI object Args : none
Title : number_nodes Usage : my $size = $tree->number_nodes Function: Returns the number of nodes Example : Returns : Args :
Title : total_branch_length Usage : my $size = $tree->total_branch_length Function: Returns the sum of the length of all branches Returns : integer Args : none
Title : height Usage : my $height = $tree->height Function: Gets the height of tree - this LOG_2($number_nodes) Returns : integer Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.