Package: aphid 1.3.6

aphid: Analysis with Profile Hidden Markov Models

Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).

Authors:Shaun Wilkinson [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
aphid/json (API)

# Install 'aphid' in R:

install.packages('aphid', repos = c('https://shaunpwilkinson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shaunpwilkinson/aphid/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

casino - Dishonest casino.
globins - Globin protein alignment.
substitution - Substitution matrices.

On CRAN:

cpp

7.00 score 22 stars 3 packages 50 scripts 491 downloads 46 exports 12 dependencies

Last updated from:cd00a45ea3. Checks:11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	176
linux-devel-x86_64	NOTE	184
source / vignettes	OK	204
linux-release-arm64	NOTE	177
linux-release-x86_64	NOTE	201
macos-release-arm64	NOTE	134
macos-release-x86_64	NOTE	251
macos-oldrel-arm64	NOTE	109
macos-oldrel-x86_64	NOTE	224
windows-devel	NOTE	162
windows-release	NOTE	136
windows-oldrel	NOTE	113
wasm-release	OK	155

Exports:align align.AAbin align.default align.DNAbin align.list backward backward.HMM backward.PHMM deriveHMM derivePHMM derivePHMM.AAbin derivePHMM.default derivePHMM.DNAbin derivePHMM.list forward forward.HMM forward.PHMM generate generate.HMM generate.PHMM logsum map plot.HMM plot.PHMM posterior posterior.HMM posterior.PHMM print.DPA print.HMM print.PHMM readPHMM train train.HMM train.PHMM unalign Viterbi Viterbi.default Viterbi.HMM Viterbi.PHMM weight weight.AAbin weight.default weight.dendrogram weight.DNAbin weight.list writePHMM

Dependencies:ape askpass curl digest kmer lattice nlme openssl phylogram qpdf Rcpp sys

The 'aphid' package for analysis with profile hidden Markov models

Rendered fromaphid-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-01-22
Started: 2017-03-21

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

Package: aphid 1.3.6

aphid: Analysis with Profile Hidden Markov Models

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