#!/usr/bin/perl -w
use strict;
my @aln;
open(FILE,"vik.fna");
while (my $line = <FILE>) {
    
    if ($line !~ /^==========/) {
	push (@aln, $line);
         }
       else {
	   open (SEQFILE, ">vik.tmp");
	    print SEQFILE join("",@aln);
	    close SEQFILE;
	     @aln = ();
             system("java -jar BMGE.jar -i vik.tmp -t AA -o tmsa.out");
             
        
          
	    }
}