sci-biology/bioperl-1.5.1-r1 is a new revision that depends on sci-libs/io_lib to enable the Staden extensions built into BioPerl. I had to remove ~alpha, ~ia64 and ~sparc keywords because io_lib is not available on these arches. Feel free to either keyword io_lib and the latest bioperl ebuild for your arch, or to remove your team from CC. The required version of io_lib is 1.8.12b-r1 (not the latest version 1.9.0-r1 which is incompatible).
~sparc added.
I suppose alpha and ia64 have little interest in bioperl, and that is fine with me. Closing.