hmm the toolbox, which has a very comprehensive hmm the matlab package, applicable to a variety of environmental use

mendelHMM
.........\em_converged.m
.........\fwdback.m
.........\gen_HMM_em.m
.........\HMM_logprob.m
.........\init_diagonal.m
.........\init_grid.m
.........\init_random.m
.........\mendelHMM.fig
.........\mendelHMM.m
.........\mk_stochastic.m
.........\multinomial_prob.m
.........\normalise.m
.........\process_options.m
.........\readme.txt
.........\resample_mendeldata.m
.........\sample_discr.m
.........\sample_HMM.m
.........\sample_MC.m
.........\set_diploidmode.m
.........\set_tetraploidmode.m
.........\view_dataseq.m
.........\view_mendeldata.m
.........\view_sampleddata.m
.........\viterbi_path.m

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