Basic pair-HMM for sequence alignment between two sequences, x and y. State M emits two letters, one from each sequence, and corresponds to the two letters being aligned together. State I_x emits a letter in sequence x that is aligned to a gap, and similarly state I_y emits a letter in sequence y that is aligned to a gap. Finding the most likely alignment according to this model by using the Viterbi algorithm corresponds to applying Needleman-Wunsch with appropriate parameters. The logarithm of the emission probability function p(.,.) at M corresponds to a substitution scoring matrix, while affine gap penalty parameters can be derived from the transition probabilities δ and ϵ (Durbin et al. 1998).