#!/usr/bin/perl -w
# Calculate the branche lengths from outgroup to the other species
# perl MyScript.pl

use strict;
use warnings;

use Bio::TreeIO;
use Bio::Tree::TreeFunctionsI;

# read in a phylip/newick format
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');

my $tree = $treeio->next_tree;
my $rootnode = $tree->get_root_node;
my @leaves = $tree->get_leaf_nodes;

my $og_id = "";
my $og = "";
my $sp_id = "";
my $sp = "";

my $distance = 0;

# Pick up the outgroup.
foreach my $node1 (@leaves) {
$og_id = $node1->id;
$og = $node1;
}

print "Outgroup: $og_id\n";

foreach my $node ( @leaves ) {

$sp_id = $node->id;
$sp = $node;

$distance = $tree->distance( -nodes => [ $og, $sp ] );

print "Distance between $og_id and $sp_id: ";
print "$distance\n";

}

exit;

(((A:5,B:5)z:2,(C:4,D:4)y:1)x:3,E:10);

[inouejun:RootToTip2]$ perl MyScript.pl
Outgroup: E
Distance between E and A: 20
Distance between E and B: 20
Distance between E and C: 18
Distance between E and D: 18
Distance between E and E: 0