There are now recombinases and target sites available in addition to FLP and FRT for use in Drosophila. The following stocks contain constructs expressing recombinases and constructs for testing recombinase activity
Most of these constructs were described in Nern et al. (2011), which discusses the merits of each system. It also discusses the toxic effects on flies of expressing cre recombinase, which, though better known than these other recombinases, presents many disadvantages.