1st file
>qppq
ATATATTTATTATTA
TATATATTATATTAT
TA
>lsl
ATTATTATTATTATT
AGGAGGAG
2nd file
>dfj
TATTATTATTTT
ATAT
>ghg
ATATATAT

##</code><code>##

>qppq
ATATATTTATTATTA
TATATATTATATTAT
TA
>dfj
TATTATTATTTT
ATAT
============
>lsl
ATTATTATTATTATT
AGGAGGAG
>ghg
ATATATAT
===========

##</code><code>##


#!/usr/bin/perl -w
use strict;
my $file1=$ARGV[0];
my $file2=$ARGV[1];
open(FILE1,"$file1");
open(FILE2,"$file2");
while (my $line1=<FILE1>){
        my $line2=<FILE2>;
        if($line1=~/^>/){
                print "$line1";
                do{
                        $line1=<FILE1>;
                        print $line1;
                }until $line1=~/^>/;
                print "$line2";
                do{
                        $line2=<FILE2>;                      
                        print $line2;
                }until $line2=~/^>/;
        }
        print "==========\n";

  }