#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Bio::Tree::DistanceFactory;
use Bio::Align::ProteinStatistics;
use Bio::TreeIO;
use Bio::Tree::Draw::Cladogram;
my $alnfile = shift @ARGV || die "need a file to run";

my $input= Bio::AlignIO->new(-format => 'fasta',
			    -file    => $alnfile);

if( my $aln = $input->next_aln ) {
 my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ'); 
 my $stats = Bio::Align::ProteinStatistics->new;
 my $distmat = $stats->distance(-align => $aln,
			         -method => 'Kimura');
 my $treeout = Bio::TreeIO->new(-format => 'newick'); 
 my $tree = $dfactory->make_tree($distmat);
 $treeout->write_tree($tree);
  my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree    => $tree,
                                             -compact => 0);
  $obj1->print(-file => "tree.eps");
} else {
 die "could not find any alignments in the file $alnfile";
}