Xiaoyu

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 $savefile = "save.phyloxml";
my $treeout = Bio::TreeIO->new(-format =>'phyloxml',
                               -file => ">$savefile");

$treeout->write_tree($subtree);

my $tree2 = Bio::TreeIO->new(-format =>'phyloxml',
                               -file => "save.phyloxml");
my $t1 = $tree2->next_tree;
my $image_output = "test.eps";
my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree   => $t1,
                                            -top    => 10,
                                             -bottom => 10,);
$obj1->print(-file => $image_output);