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Gmane
From: Jason Stajich <jason.stajich <at> gmail.com>
Subject: Re: Asking
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 13th December 2012 04:05:29 UTC (over 4 years ago)
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" 
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 @filenames = glob("*.txt");
> foreach my $filename (@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
 
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