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
Config/pak/sysreqs: make libjpeg-dev libssl-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2026-01-23 02:04:50 UTC
RemoteUrl: https://github.com/shaunpwilkinson/aphid
RemoteRef: HEAD
RemoteSha: cd00a45ea36d9b26c02e68a33ffa7f5831aef873
NeedsCompilation: yes
Packaged: 2026-06-22 07:22:07 UTC; root