FIG. 1.—

SMUVE, a generalized pair HMM architecture. Match state (M) emits a pair of nucleotides to the alignment via the K2P model, whereas indel states (U and V) emit nucleotides to only one sequence based on either a zeta or geometric distribution. Transition probabilities are evenly distributed out of each node unless otherwise noted; τ = 1/(a + 1) and η = e^−2rt.