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aphid
View on CRAN: Click
here
Download and install aphid package within the R console
Install from CRAN:
install.packages("aphid")
Install from Github:
library("remotes")
install_github("cran/aphid")
Install by package version:
library("remotes")
install_version("aphid", "1.3.5")
Attach the package and use:
library("aphid")
Maintained by
Shaun Wilkinson
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-06-24
Latest Update: 2022-12-05
Description:
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).
How to cite:
Shaun Wilkinson (2017). aphid: Analysis with Profile Hidden Markov Models. R package version 1.3.5, https://cran.r-project.org/web/packages/aphid
Previous versions and publish date:
Other packages that cited aphid R package
View aphid citation profile
Other R packages that aphid depends,
imports, suggests or enhances
Functions, R codes and Examples using
the aphid R package
Some associated functions: Viterbi . align . aphid . backward . casino . deriveHMM . derivePHMM . forward . generate . globins . logsum . map . plot.HMM . plot.PHMM . posterior . print . readPHMM . substitution . train . unalign . weight . writePHMM .
Some associated R codes: RcppExports.R . Viterbi.R . align.R . aphid.R . backward.R . data.R . deriveHMM.R . derivePHMM.R . forward.R . generate.R . plot.R . posterior.R . print.R . read.R . train.R . utils.R . weight.R . write.R . Full aphid package functions and examples
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