die "Usage: $0 InputFile1 InputFile2 OutputFile\n"
    unless @ARGV==3;
my ($InputFile1, $InputFile2, $OutputFile3) = @ARGV;
# ... rest of the code here

##</code><code>##

sub process_files {
    my ($InputFile1, $InputFile2, $OutputFile3) = @_;
    # ... rest of your code here
}

##</code><code>##

my @filesets = (
    { input1 => "edited_archaea_master_list.txt",
      input2 =>
        "testprefix172_single_line_nostrains_aligned_gaps_test.meg",
      output => "rearrangement_out_test.txt" },
    # ... more file sets here
);

for my $fileset (@filesets) {
    process_files( $fileset->{input1}, $fileset->{input2},
        $fileset->{output} );
}