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