TreeI interface is implemented at the organism level for efficient data processing. Its advanced features and functionality make it an ideal tool for managing large datasets and enhancing research in various fields.
Using Bio::Taxon in combination with Bio::Tree::Tree is simple. You can import a tree from a TreeIO, and then get nodes, pull out the root, and perform various other functions. For example, you can use the Bio::TreeIO module to import a newick formatted tree file with the code:
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
From there, you can get access to the nodes in the tree and work with them using the following code:
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;
my @leaves = $tree->get_leaves;
Overall, Bio::Taxonomy::Tree is a useful software tool for managing and manipulating taxonomic information in a tree structure. However, it is important to follow the recommendation to use Bio::Taxon in combination with Bio::Tree::Tree instead, due to the deprecation of this module.
Version 1.6.0: N/A