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} );
}