It really depends on the subfield. Sequence-based genomics is very highly Perl-dependent even today. BioPerl is pretty much the standard library for that even though BioPython, etc. are beginning to take over. Other subfields such as differential sequence abundance which are more about the statistics rather than the raw sequence tend to be R-centered thanks to Bioconductor.

I think by your definitions there are sub-subfields then ;) In my neck of the woods sequence based stuff has java & c doing a lot of the heavy lifting.