Okay, sorry I was trying to keep it succinct. Thanks for the interest. The original data is multiple alignments of DNA sequences, in blocks- 4 lines to a block corresponding to 4 different species. Each line contains the position of the sequences (and also other descriptives in the first few fields). The last field is the sequence. So by 'keep' I mean dont filter/remove and place that block into the hash I described earlier, so I can then process elsewhere in the program. The filtering is based on the second file containing positions of the first sequence in the blocks (the reference sequence) which I need to 'keep'. Is this more clear?