The only person I've worked with over the past 20+ years who used Perl was a bioinformatics guru. When he taught students in the lab, however, he'd switch to Python.
As the cost of sequencing keeps coming down, we sequence deeper, and the computational demand goes up. Plain-text is replaced with binary formats, and most of the heavy lifting is now done by compiled libraries. The benefits of Perl aren't really relevant anymore, and given the choice most of us simply prefer writing Python or R.