...
my $outfile = '/path/to/file/to/create';
open my $fh, '>', $outfile or die "Cannot create $outfile, $!\n";
my $treeout = Bio::TreeIO->new(-format => 'newick', -fh => $fh);
...

##</code><code>##

...
my $outfile = '/path/to/file/to/create';
my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">$outfile");
...