Package: aphid 1.3.3.9000

Shaun Wilkinson

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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aphid.pdf |aphid.html✨
aphid/json (API)

# Install 'aphid' in R:
install.packages('aphid', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

6.56 score 22 stars 3 packages 37 scripts 469 downloads 46 exports 12 dependencies

Last updated 4 months agofrom:3cbfb0e051. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-win-x86_64NOTENov 16 2024
R-4.5-linux-x86_64NOTENov 16 2024
R-4.4-win-x86_64NOTENov 16 2024
R-4.4-mac-x86_64NOTENov 16 2024
R-4.4-mac-aarch64NOTENov 16 2024
R-4.3-win-x86_64NOTENov 16 2024
R-4.3-mac-x86_64NOTENov 16 2024
R-4.3-mac-aarch64NOTENov 16 2024

Exports:alignalign.AAbinalign.defaultalign.DNAbinalign.listbackwardbackward.HMMbackward.PHMMderiveHMMderivePHMMderivePHMM.AAbinderivePHMM.defaultderivePHMM.DNAbinderivePHMM.listforwardforward.HMMforward.PHMMgenerategenerate.HMMgenerate.PHMMlogsummapplot.HMMplot.PHMMposteriorposterior.HMMposterior.PHMMprint.DPAprint.HMMprint.PHMMreadPHMMtraintrain.HMMtrain.PHMMunalignViterbiViterbi.defaultViterbi.HMMViterbi.PHMMweightweight.AAbinweight.defaultweight.dendrogramweight.DNAbinweight.listwritePHMM

Dependencies:apeaskpasscurldigestkmerlatticenlmeopensslphylogramqpdfRcppsys

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

Shaun Wilkinson

Rendered fromaphid-vignette.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2019-03-15
Started: 2017-03-21

Readme and manuals

Help Manual

Help pageTopics
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
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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