Package Bio :: Package HMM :: Module Trainer
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Module Bio.HMM.Trainer

Provide trainers which estimate parameters based on training sequences.

These should be used to 'train' a Markov Model prior to actually using it to decode state paths. When supplied training sequences and a model to work from, these classes will estimate paramters of the model.

This aims to estimate two parameters:

* a_{kl} -- the number of times there is a transition from k to l in the training data.

* e_{k}(b) -- the number of emissions of the state b from the letter k in the training data.
Classes
AbstractTrainer Provide generic functionality needed in all trainers.
BaumWelchTrainer Trainer that uses the Baum-Welch algorithm to estimate parameters.
KnownStateTrainer Estimate probabilities with known state sequences.
TrainingSequence Hold a training sequence with emissions and optionally, a state path.

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