Running StochHMM Application

##StochHMM - Stochastic Hidden Markov Model Framework

##Usage: StochHMM -model <model_file> -seq <seq_file> [options] Example: ./StochHMM -model Dice.hmm -seq Dice.fa -viterbi -gff

##Command Line options:

###Files: StochHMM requires a sequence file and a model file -model import model file -seq import sequence file in fasta format

###Non-stochastic Decoding: Different algorithms available for decoding -viterbi performs viterbi traceback -nbest performs the N-best Viterbi and return # number of paths

###Posterior Decoding: -posterior Calculates posterior probabilities

###Stochastic Decoding -stochastic : Performs stochastic decoding using algorithm type. Must also set number of repetitions Types: viterbi Uses viterbi scores to calculate stochastic traceback probabilities forward Uses forward scores to calculate stochastic traceback probabilities posterior Uses posterior scores to calculate stochastic traceback probabilities

-repetitions <int>	Number of stochastic tracebacks to perform

###Output options: -gff prints path in GFF format -path prints state path according to state number -label prints state path as labels -trellis print the trellis values

Written by Paul Lott at University of California, Davis Please direct any questions, suggestions or bugs reports to Paul Lott at [email protected]

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