View difference between Paste ID: fc4715a1 and

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+use lib '/home/egstation/applications/bioperl-live'; #we check out the latest SVN code
 use Bio::TreeIO;
 use Bio::Tree::Tree;
 use Data::Dumper;
 use Bio::Tree::Draw::Cladogram;
 
 
 my $treeio = Bio::TreeIO->new(-file   => "HSF.phyloxml",
                             -format => "phyloxml");
 my $tree = $treeio->next_tree;
 my @nodes = $tree->get_nodes;
 my $nodeid;
 for (my $i=0; $i<=$#nodes;$i++){
     if($nodes[$i]->id eq 'LOC_Os08g43334.2'){
         $nodeid=$i;
     }
 }
 
 my $ance = $nodes[$nodeid]->ancestor;
 my $count=0;
 for my $child($ance->get_all_Descendents){
     if($child->id){
         $count++;
     }
 }
 my $copy = $ance;
 while($count<5){
     $count=0;
     my $new_anc = $copy->ancestor;
     for my $child($new_anc->get_all_Descendents){
         if($child->id){
             $count++;
         }
     }
     $copy = $new_anc;
 }
 my @children;
 for my $child($copy->get_all_Descendents){
     push(@children,$child);
 }
 
 my $new_root = $tree->get_lca( -nodes => \@children);
 my $subtree = Bio::Tree::Tree->new(-root => $new_root, -nodelete => 1);
 
 my $image_output = "test.eps";
 my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree   => $subtree,
                                             -top    => 10,
                                              -bottom => 10,);
 $obj1->print(-file => $image_output);