Tim's speed ups are applied: We now have - [localhost:~/data] birney% time perl -I ~/src/bioperl-live/ fasta2fasta.pl < rod.fa 13.470u 1.220s 0:16.65 88.2% 0+0k 0+0io 0pf+0w [localhost:~/data] birney% time perl -I ~/src/bioperl-1.1.0 fasta2fasta.pl < rod.fa 49.180u 3.070s 1:01.11 85.5% 0+0k 0+0io 0pf+0w Which is not bad at all!