Bio.HMM package

Submodules

• Bio.HMM.DynamicProgramming module
  • AbstractDPAlgorithms
    • AbstractDPAlgorithms.__init__()
    • AbstractDPAlgorithms.forward_algorithm()
    • AbstractDPAlgorithms.backward_algorithm()
  • ScaledDPAlgorithms
    • ScaledDPAlgorithms.__init__()
  • LogDPAlgorithms
    • LogDPAlgorithms.__init__()
• Bio.HMM.MarkovModel module
  • MarkovModelBuilder
    • MarkovModelBuilder.DEFAULT_PSEUDO
    • MarkovModelBuilder.__init__()
    • MarkovModelBuilder.get_markov_model()
    • MarkovModelBuilder.set_initial_probabilities()
    • MarkovModelBuilder.set_equal_probabilities()
    • MarkovModelBuilder.set_random_initial_probabilities()
    • MarkovModelBuilder.set_random_transition_probabilities()
    • MarkovModelBuilder.set_random_emission_probabilities()
    • MarkovModelBuilder.set_random_probabilities()
    • MarkovModelBuilder.allow_all_transitions()
    • MarkovModelBuilder.allow_transition()
    • MarkovModelBuilder.destroy_transition()
    • MarkovModelBuilder.set_transition_score()
    • MarkovModelBuilder.set_transition_pseudocount()
    • MarkovModelBuilder.set_emission_score()
    • MarkovModelBuilder.set_emission_pseudocount()
  • HiddenMarkovModel
    • HiddenMarkovModel.__init__()
    • HiddenMarkovModel.get_blank_transitions()
    • HiddenMarkovModel.get_blank_emissions()
    • HiddenMarkovModel.transitions_from()
    • HiddenMarkovModel.transitions_to()
    • HiddenMarkovModel.viterbi()
• Bio.HMM.Trainer module
  • TrainingSequence
    • TrainingSequence.__init__()
  • AbstractTrainer
    • AbstractTrainer.__init__()
    • AbstractTrainer.log_likelihood()
    • AbstractTrainer.estimate_params()
    • AbstractTrainer.ml_estimator()
  • BaumWelchTrainer
    • BaumWelchTrainer.__init__()
    • BaumWelchTrainer.train()
    • BaumWelchTrainer.update_transitions()
    • BaumWelchTrainer.update_emissions()
  • KnownStateTrainer
    • KnownStateTrainer.__init__()
    • KnownStateTrainer.train()
• Bio.HMM.Utilities module
  • pretty_print_prediction()

Module contents

A selection of Hidden Markov Model code.