API for aphid
Analysis with Profile Hidden Markov Models

Global functions
.ViterbiD	Source code
.ViterbiH	Source code
.ViterbiP	Source code
.ViterbiPP	Source code
.a2s	Source code
.acount	Source code
.alphadetect	Source code
.arc	Source code
.atab	Source code
.backwardH	Source code
.backwardP	Source code
.chord	Source code
.d2s	Source code
.decimal	Source code
.diamond	Source code
.digest	Source code
.disambiguateAA	Source code
.disambiguateDNA	Source code
.ecount	Source code
.ellipse	Source code
.encodeAA	Source code
.encodeCH	Source code
.encodeDNA	Source code
.forwardH	Source code
.forwardP	Source code
.insert	Source code
.insertlengths	Source code
.isAA	Source code
.isDNA	Source code
.logdetect	Source code
.map	Source code
.point	Source code
.probAA	Source code
.probDNA	Source code
.s2a	Source code
.s2d	Source code
.streak	Source code
.tabulateAA	Source code
.tabulateCH	Source code
.tabulateDNA	Source code
.trim	Source code
.whichmax	Source code
Viterbi	Man page Source code
Viterbi.HMM	Man page
Viterbi.PHMM	Man page Source code
Viterbi.default	Man page Source code
align	Man page Source code
align.AAbin	Man page Source code
align.DNAbin	Man page Source code
align.default	Man page Source code
align.list	Man page Source code
aphid	Man page
backward	Man page Source code
backward.HMM	Man page
backward.PHMM	Man page Source code
casino	Man page
deriveHMM	Man page Source code
derivePHMM	Man page Source code
derivePHMM.AAbin	Man page Source code
derivePHMM.DNAbin	Man page Source code
derivePHMM.default	Man page Source code
derivePHMM.list	Man page Source code
forward	Man page Source code
forward.HMM	Man page
forward.PHMM	Man page Source code
generate	Man page Source code
generate.HMM	Man page
generate.PHMM	Man page
globins	Man page
logsum	Man page Source code
map	Man page Source code
plot.HMM	Man page Source code
plot.PHMM	Man page Source code
posterior	Man page Source code
posterior.HMM	Man page Source code
posterior.PHMM	Man page Source code
print	Man page
print.DPA	Man page Source code
print.HMM	Man page Source code
print.PHMM	Man page Source code
readPHMM	Man page Source code
substitution	Man page
train	Man page Source code
train.HMM	Man page Source code
train.PHMM	Man page Source code
unalign	Man page Source code
weight	Man page Source code
weight.AAbin	Man page Source code
weight.DNAbin	Man page Source code
weight.default	Man page Source code
weight.dendrogram	Man page Source code
weight.list	Man page Source code
writePHMM	Man page Source code