Perl is mostly used in the niches it's traditionally good at, munging data or cleaning it up with quick to write one-off scripts. The data is then fed into a higher performance C or Java program for the actual analysis.
They tried to use Python for that kind of task, but the language is stricter than Perl (you end up writing lots of exception handling code) and the text gobbling faculties are just ever so slightly not as good and it ends up just being easier and quicker to Perl the problem away. However, the newer folks are coming in not knowing Perl at all and it's likely it will simply go away in a few years and everything will be done in Python anyways.
Python and Java tend to be used on the back-end of the web reporting systems they build since there's better server-side support and tooling for that case. And I think some of the analytic tools are cross platform Java desktop clients.
As someone who knows the author of the post, that is mostly true ;)
In all seriousness, while I generally agree with your sentiments I don't think that Perl is dead within Bioinformatics. Not least since major data providers, e.g. Ensembl, write their tools in Perl.
Oh I know it still exists, but while this is admittedly anecdotal on my part (and likely heavily biased by the institutions I've been a part of) I haven't seen a single new person who defaults to Perl in a very, very, very long time.
And to be clear, I'm not trying to rip the author or the article, it just seems ... oddly timed, like writing a contemporary article on how to use COBOL in the business computing space.
I'm not sure I agree with that, however.
Perl 6 is probably best described as a dialect. The look and design of the language are very Perl-ish, but some of the key sore points from Perl 5 (OO, concurrency, etc) are addressed and it has added a number of killer features. This is not Python 2->32; it is a major overhaul of the language, with no backwards compat beyond a suggested perl 5-compatible layer (I believe this is called 'v5').
The article touches upon a few (Grammars for instance), but I personally think the concurrency work will also be a real draw.
The other key difference is that Perl 6 is actually a specification with an official test suite and Grammar (STD). I believe the specs indicate that anything that passes the test suite can be deemed to support 'Perl 6', which really opens up the use of various backends. The Rakudo Perl 6 implementation has support for three (MoarVM, Parrot, and JVM).
I've been in the bioinformatics space for about 13 years now and I've only come a small handful of perl scripts, all of which have been legacy programs. Even when I started in the field, perl was viewed as somewhat anachronistic. All of the end-user software I've written (read: For researchers) has been in R, Java and a wee bit of scala.
These days all of the researchers I know are using some combo of R, Python and to a lesser extent MATLAB. Many have useful C and/or Java (and/or Scala) skills as well.
My personal experience is obviously not exhaustive but I find it hard to believe that many people are using Perl these days, and IMO that's a matter of good riddance.