#2
my $alnio = Bio::AlignIO->new('-file'=> 'out_file','-format' => 'clustalw');

my $dfactory = Bio::Tree::DistanceFactory->new('-method' => 'NJ');

my $stats = Bio::Align::ProteinStatistics->new;

my $treeout = Bio::TreeIO->new('-format' => 'newick');

while( my $aln = $alnio->next_aln ) 
{
 my $mat = $stats->distance('-method' => 'Kimura',
                            '-align'  => $aln);
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}