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).

Version:	1.3.5
Depends:	R (≥ 3.0.0)
Imports:	graphics, openssl, kmer (≥ 1.0.0), Rcpp (≥ 0.12.5), stats
LinkingTo:	Rcpp
Suggests:	ape (≥ 4.0), knitr, qpdf, rmarkdown, testthat
Published:	2022-12-05
DOI:	10.32614/CRAN.package.aphid
Author:	Shaun Wilkinson [aut, cre]
Maintainer:	Shaun Wilkinson <shaunpwilkinson at gmail.com>
BugReports:	https://github.com/shaunpwilkinson/aphid/issues
License:	GPL-3
URL:	https://github.com/shaunpwilkinson/aphid
NeedsCompilation:	yes
SystemRequirements:	GNU make
Citation:	aphid citation info
Materials:	README
In views:	Phylogenetics
CRAN checks:	aphid results

Documentation:

Reference manual:	aphid.pdf
Vignettes:	Introduction to the aphid package

Downloads:

Package source:	aphid_1.3.5.tar.gz
Windows binaries:	r-devel: aphid_1.3.5.zip, r-release: aphid_1.3.5.zip, r-oldrel: aphid_1.3.5.zip
macOS binaries:	r-release (arm64): aphid_1.3.5.tgz, r-oldrel (arm64): aphid_1.3.5.tgz, r-release (x86_64): aphid_1.3.5.tgz, r-oldrel (x86_64): aphid_1.3.5.tgz
Old sources:	aphid archive

Reverse dependencies:

Reverse imports:

coil, debar, insect

Linking:

Please use the canonical form https://CRAN.R-project.org/package=aphid to link to this page.