Man pages for aphid
Analysis with Profile Hidden Markov Models
| align | Multiple sequence alignment in R. |
| aphid | The 'aphid' package for analysis with profile hidden Markov... |
| backward | The backward algorithm. |
| casino | Dishonest casino. |
| deriveHMM | Derive a standard hidden Markov model from a set of... |
| derivePHMM | Derive a profile hidden Markov model from sequences. |
| forward | The forward algorithm. |
| generate | Generate random sequences from a model. |
| globins | Globin protein alignment. |
| logsum | Sum of logged probabilities. |
| map | Optimized profile HMM construction. |
| plot.HMM | Plot standard hidden Markov models. |
| plot.PHMM | Plot profile hidden Markov models. |
| posterior | Posterior decoding. |
| Print summary methods. | |
| readPHMM | Import profile hidden Markov models into R. |
| substitution | Substitution matrices. |
| train | Iterative model refinement. |
| unalign | Deconstruct an alignment. |
| Viterbi | The Viterbi algorithm. |
| weight | Sequence weighting. |
| writePHMM | Export profile hidden Markov models as text. |
