Somehow the order between the original fasta file and the results PhymmBL do not align. Re-writing script to account for this -- however, this will be much slower.
 11 If it is possible to revert to the previous method, the "count" variable would need to be re-introduced (start value == 1, first line in PhymmBL results file is a header) and the
 12 increment count for each time