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 plott@ucdavis.edu