[Bioperl-l] distances between leaf nodes

Jeffrey Detras jdetras at gmail.com
Fri Mar 5 01:17:40 EST 2010


Hi,

I am new at using the Bio::TreeIO module specifically using the newick
format for a phylogenetic analysis. The sample_tree attached is
Newick-formatted tree. My objective is to get all the distances between all
the leaf nodes. I copied examples of the code from
http://www.bioperl.org/wiki/HOWTO:Trees but it does not tell me much (to my
knowledge) so that I understand how to assign the right array value for the
nodes/leaves. The message would say must provide 2 root nodes.

Here is what I have right now:

#!/usr/bin/perl -w
 use strict;

 my $treefile = 'sample_tree';
 use Bio::TreeIO;
 my $treeio = Bio::TreeIO->new(-format => 'newick',
                                 -file => $treefile);

 while (my $tree = $treeio->next_tree) {
         my @leaves = $tree->get_leaf_nodes;
         for (my $dist = $tree->distance(-nodes => \@leaves)){
                 print "Distance between trees is $dist\n";
         }
 }

Thanks,
Jeff
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