sub msa{
# perform clustalw multiple sequence alignment 
	my ($maid, $maid_dir)=@_;
	my $contig1 = "$maid_dir\\$maid"."contig1";
	my $contig1_out = "$maid_dir\\$maid"."contig1.aln";	
	my $contig2 = "$maid_dir\\$maid"."contig2";
	my $contig2_out = "$maid_dir\\$maid"."contig2.aln";
	my $out1 = "$maid_dir\\$maid"."contig1.txt";
	my $out2 = "$maid_dir\\$maid"."contig2.txt";
	if($contig1=~ m/contig1$/){			
		my @command_contig1 = ('c:\\Clustalw\clustalw2.exe', $contig1, '/align', "/outfile=$contig1_out");    
		system(@command_contig1);	
	}
	if($contig1=~ m/contig2$/){
		my @command_contig2 = ('c:\\Clustalw\clustalw2.exe', $contig2, '/align', "/outfile=$contig2_out"); 
		system(@command_contig2);
	}
	return ($out1, $out2);
}