I just tracked down one documentation error for Bio::Tools::Sim4::Results.pm. The synopsis says: # to preset the order of EST and genomic file as given on the sim4 # command line: $sim4 = Bio::Tools::Sim4::Results->new(-file => 'result.sim4', -estisfirst => 1); But this doesn't work as intended because the attribute "estisfirst" is ignored. It should have been "estfirst".