Perl script that uses the Ensembl Compara Perl API to print the protein tree with the stable id ENSGT00390000003602

exercise5_compara.pl

#!/usr/bin/env perl

# Print the protein tree with the stable id ENSGT00390000003602

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
);

my $gta = $registry->get_adaptor('multi', 'compara', 'GeneTree');
my $genetree = $gta->fetch_by_stable_id("ENSGT00390000003602");
$genetree->print_tree(); # prints the tree in ASCII format
print "\n\n";
print $genetree->newick_format('simple'),"\n\n"; # prints the tree in Newick format
print $genetree->nhx_format('full'),"\n\n"; # prints the tree in nhx format
print $genetree->nhx_format('display_label_composite'),"\n\n"; # includes the gene names and species names in nhx format