#!/usr/bin/perl
BEGIN {$ENV{PAL2NALDIR} = "pal2nal"}
use Bio::Tools::Run::Alignment::Pal2Nal;
use Bio::AlignIO;
use Bio::SeqIO;

#Input protein alignment
#CLUSTAL W (1.82) multiple sequence alignment

#BC070280        MVGSLNCIVAVSQNMGIGKNGDLPWPPL
#pseudogene      ----LNCIVNDSQKMGIIRNGDLP-PQL

my $alignio = Bio::AlignIO->new(-file => 'test1.aln',
		 		-format => 'Clustalw');	
my $alnpr = $alignio->next_aln;

#Input DNA sequences
$seqio = Bio::SeqIO->new( '-format' => 'fasta' , -file => 'test1.txt');
	
	my $DNA1 = $seqio->next_seq();
	my $DNA2 = $seqio->next_seq();

#my $DNA1 = 'ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCCTGGCCACCGCTC';
#my $DNA2 = 'CTAAACTGCATTGTCAATGATTCCCAGAAGATGGGCATCATCAGGAATGGGGACCTGCCCCCTCAGCTC';


# Make a Pal2Nal factory
$factory = Bio::Tools::Run::Alignment::Pal2Nal->new();
# Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide file

my $alnDP = $factory->run($alnpr, [$DNA1,$DNA2]);

#output the result with phylip format

my $in  = Bio::AlignIO->new(-file   => $alnDP,
                             -format => 'Clustalw');
my $out = Bio::AlignIO->new(-file   => ">out.phy" ,
                            -format => 'phylip');
while ( my $aln = $in->next_aln() ) {
        $out->write_aln($aln);
    }