The increased availability of genome sequences of closely related organisms has generated much interest in utilizing homology to improve the accuracy of gene prediction programs. Generalized pair hidden Markov models (GPHMMs) have been proposed as one means to address this need. However, all GPHMM implementations currently available are either closed-source or the details of their operation are not fully described in the literature, leaving a significant hurdle for others wishing to advance the state of the art in GPHMM design.