Bio::Tree::NodeI - Interface describing a Tree Node
# get a Tree::NodeI somehow # like from a TreeIO use Bio::TreeIO; # read in a clustalw NJ in phylip/newick format my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'file.dnd'); my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes my $rootnode = $tree->get_root_node; # process just the next generation foreach my $node ( $tree->each_Descendent() ) { print "branch len is ", $node->branch_length, "\n"; } # process all the children foreach my $node ( $tree->get_Descendents() ) { if( $node->is_Leaf ) { print "node is a leaf ... "; } print "branch len is ", $node->branch_length, "\n"; }
A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid branch length.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : add_Descendent Usage : $node->add_Descendant($node); Function: Adds a descendent to a node Returns : number of current descendents for this node Args : Bio::Node::NodeI
Title : each_Descendent Usage : my @nodes = $node->each_Descendent; Function: all the descendents for this Node (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Tree::NodeI objects Args : none
Title : get_Descendents Usage : my @nodes = $node->get_Descendents; Function: Recursively fetch all the nodes and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Tree::NodeI objects Args : none
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none
Title : descendent_count Usage : my $count = $node->descendent_count; Function: Counts the number of descendents a node has (and all of their subnodes) Returns : integer Args : none
Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none
Title : height Usage : my $len = $node->height Function: Returns the height of the tree starting at this node. Height is the maximum branchlength. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none
Title : branch_length Usage : $obj->branch_length() Function: Example : Returns : value of branch_length Args : newvalue (optional)
Title : id Usage : $obj->id($newval) Function: Example : Returns : value of id Args : newvalue (optional)
Title : description Usage : $obj->description($newval) Function: Example : Returns : value of description Args : newvalue (optional)
Title : bootstrap Usage : $obj->bootstrap($newval) Function: Example : Returns : value of bootstrap Args : newvalue (optional)
Title : ancestor Usage : my $node = $node->ancestor; Function: Get/Set a Node's ancestor node Returns : Null if this is top level node 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.