Man pages for aphid
Analysis with Profile Hidden Markov Models

alignMultiple sequence alignment in R.
aphidThe 'aphid' package for analysis with profile hidden Markov...
backwardThe backward algorithm.
casinoDishonest casino.
deriveHMMDerive a standard hidden Markov model from a set of...
derivePHMMDerive a profile hidden Markov model from sequences.
forwardThe forward algorithm.
generateGenerate random sequences from a model.
globinsGlobin protein alignment.
logsumSum of logged probabilities.
mapOptimized profile HMM construction.
plot.HMMPlot standard hidden Markov models.
plot.PHMMPlot profile hidden Markov models.
posteriorPosterior decoding.
printPrint summary methods.
readPHMMImport profile hidden Markov models into R.
substitutionSubstitution matrices.
trainIterative model refinement.
unalignDeconstruct an alignment.
ViterbiThe Viterbi algorithm.
weightSequence weighting.
writePHMMExport profile hidden Markov models as text.
aphid documentation built on Oct. 9, 2018, 9:03 a.m.