I’ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May. I know
MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc.
Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might
be required? (I haven’t checked the 3.0 beta version yet)