Re: Asking

You want the reroot function. Have you tried reading the howtos on the website already. 
Node is a node in the tree. There are several functions to find a node or iterate through all the ones in the tree

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Dec 12, 2012, at 7:30 PM, "Xing-Xing Shen" <shenxingxing2010 <at> gmail.com> wrote:

> Drear Jason 
> I am a green hand in learning Bioperl. Now, I met a problem about how to define outgroup for a set of newick trees.
> 
> My codes below:
> #!/usr/bin/perl
> use Bio::TreeIO;
> use Bio::Tree::NodeI;
> use Bio::Tree::Tree;
> my  <at> filenames = glob("*.txt");
> foreach my $filename ( <at> filenames) {
>    my $treeio = Bio::TreeIO->new('-format' => 'newick', '-file'   => "$filename");
>    while( my $tree = $treeio->next_tree ) {
>       $tree->set_root_node("$node"); # what might $node mean?
>        ..........
>        ..........
>    }
> }
> 
> 
> With best,
> 
> Xing-Xing Shen