Python - All a Scientist Needs
He used Python to gather data, organize it, and run computations against it.
Unfortunately, Biopython isn't as nice, as large, or as well organized as BioPerl. Despite this, he still preferred to code in Python over Perl.
He also made use of Matplotlib and Numpy.
He rewrote some performance critical code in C and interfaced with it using SWIG. This saved about a week of computation time.