Ok, that helps. If the tags in your input file are guaranteed to be unique, it's easy. Put them in a hash with the frequencies as the values, and then sort on the values. In this example, %tags is the hash that stores the tags and their corresponding values, and then it's sorted on the values numerically, largest to smallest. The sub make_unique_string() creates the unique key for your output file from the tag and freq.

my %tags;
while(<$input_file_descriptor>){
  # do stuff to skip headers and blank lines
  chomp;
  my( $tag, $freq ) = split /\s+/;
  $tags{$tag} = $freq;
}

for my $tag (sort { $tags{$b} <=> $tags{$a} } keys %tags ){
  my $freq = $tags{$tag}; # to clarify things below
  my $unique_string = make_unique_string($tag, $freq);
  print ">$unique_string\t$tag\t$freq\n";
}
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