$/ = '</species>.$/;
my $prev_rec='';
while (<INFILE>) {
  next if ($_ eq $prev_rec);
  $prev_rec = $_;
  # process $_ somehow as it is unique
}

##</code><code>##

use Data::Dumper;

if (Dumper(\%struct1) eq Dumper(\%struct2)) {
  do something;
}