Package: aphid
Type: Package
Title: Analysis with Profile Hidden Markov Models
Version: 1.3.6
Authors@R: person("Shaun", "Wilkinson", email = "shaunpwilkinson@gmail.com",
    role = c("aut", "cre"))
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
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).
License: GPL-3
URL: https://github.com/shaunpwilkinson/aphid
BugReports: https://github.com/shaunpwilkinson/aphid/issues
LazyData: TRUE
Encoding: UTF-8
SystemRequirements: GNU make
Depends: R(>= 3.0.0)
Imports: graphics, openssl, kmer (>= 1.0.0), qpdf, Rcpp (>= 0.12.5),
        stats
Suggests: ape (>= 4.0), knitr, rmarkdown, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
RoxygenNote: 7.3.1
NeedsCompilation: yes
Packaged: 2026-01-22 21:37:44 UTC; wilderlab
Repository: CRAN
Date/Publication: 2026-01-23 06:41:06 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-25 18:29:47 UTC; unix
Archs: aphid.so.dSYM
