17 years later, Perl still seems to be the go-to tool in bioinformatics.
In my experience as a global contractor, there are at least big players who use Perl exclusively, and in Perl irc channels i see bio informatics people very regularly.
UCSC has switched from teaching Perl to teach Python in intro bioinformatics classes (they get 5-10 new PhD students a year, plus at least that many masters students, I think?). Nobody that I encountered at my postdoc institution used Perl, maybe about 60 people who programmed, and I knew enough of ~20 people's habits to know their programming choices. R, Python, and C/C++ were commonplace, with a few weirdos using Ruby, and of course lots of shell, awk, and sed glue to keep it all together. The Broad has been somewhat successful on shoving Java into people's pipelines with GATK and Picard, but it's not a welcome addition to many people's habits, and I haven't encountered any significantly used project around next gen sequencing that is based in Perl. For example, in the RNA world, all the common tools like Tophat, Mapsplice, and ChimeraScan all use Python in ways that Perl would have been used 10-15 years ago.
I have active collaborations with about five different labs that also have in-house informatics for everything from microarrays, to ChIP-Seq, to RNA-seq, exome to whole-genome resequencing, and nobody uses Perl for any of it.
That said, it's really easy to collaborate with lots of informatics people and never even need to know what they use internally. What's this about contracting in bioinformatics? I've never encountered such a thing.
As for contracting: Oftentimes bioinformatics people will realize that they're not good programmers at all and call in people to help make their code less of a rat's nest and learn from them at the same time. It happens quite often here in Europe.
BioPerl: https://github.com/bioperl/bioperl-live
BioPython: https://github.com/biopython/biopython
People using BioPerl just use it to get something done and don't care to join the larger community. In Perl we call it the DarkPAN.
Meanwhile anyone wishing to use Python will at least have needed to make an effort to learn the language, since there is nothing else quite like it; and as such probably more likely to invest further effort.
But, i do admit that this is conjecture.