use strict;
use warnings;

use Bio::AlignIO;
use Bio::Align::ProteinStatistics;
use Bio::Tree::DistanceFactory;
use Bio::TreeIO;

my $alnio = Bio::AlignIO->new(-file => 'outfile.fasta', -format=>'fasta');

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);
}