Fig 1. Hidden Potts model architecture.

Squares are conserved match states and diamonds are insert states. No delete states exist. Silent begin and end states are represented by circles. An HPM is a hybrid between a Potts model and a pHMM: correlated character generation (including deletion “characters” rather than delete states) in match columns (consensus sites in an MSA) comes from a Potts distribution (dotted orange arrows), while transition probabilities linking states and site-independent character emissions in unaligned insert columns come from a pHMM (solid and dashed black arrows, respectively).