| N | length of the data set |
| K | number of states |
| m | dimension of data vectors, y_t |
| nu | recombination rate |
| TransP[1:K,1:K] | matrix of transition probabilities [S_(t+1),S_t] |
| P0[1:K]' | initial probabilities |
| D[1:m,1:N] | training data: D=(y_1,...,y_N) |
| Dgen[1:m,1:N] | test data: D=(y_1,...,y_N) |
| ScaleFact[1:N] | scaling factors, computed in the forward path |
| Alpha[1:K,1:N] | array of alpha_t(s_t), computed in the forward path |
| Beta[1:K,1:N] | array of beta_t(s_t), computed in the backward path |
| PSD[1:K,1:N] | array of posterior probabilities P(s_t|D) |
| PSSD[1:K,1:K,1:(N-1)] | array of posterior probabilities P(s_t,s_(t+1)|D) |
| EmissionP[1:K,1:N] | array of emission probabilities for all states |
| HMM_O | Object: Emission model of the HMM |
| alpha_prior, beta_prior | prior values of the hyperparameters |
| alpha_post, beta_post | posterior values of the hyperparameters |