Perl and bioinformatics

I think this is essentially correct. The problem in Bioinformatics, as in many areas, is that much of the early work was done in widely separated groups who weren't coordinating much. The result was a bunch of really good tools that don't play nicely together because they speak different languages. Rather than try to rewrite everything to work together perfectly, they stuck it together with a glue layer written in Perl. And of course once you have a setup in Perl that's the only thing that understands all the different languages, it's the natural choice to build new tools.

The result is that Bioperl now has literally hundreds of modules. Many of them are rather special purpose, but taken together they give you a very nice toolbox for solving your Bioinformatics problems. They may be a bit heavyweight- for some simple problems I find it's easier to write my own, lightweight solution than to read through the reams of Bioperl documentation to find the tool that does what I want- but that's the price you pay for the power and flexibility.