Analysis with Profile Hidden Markov Models R package aphid version 1.3.6 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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). Software Depends: R(>= 3.0.0) Imports: graphics, openssl, kmer (>= 1.0.0), qpdf, Rcpp (>= 0.12.5), stats LinkingTo: Rcpp Suggests: ape (>= 4.0), knitr, rmarkdown, testthat Shaun Wilkinson <shaunpwilkinson@gmail.com> Comprehensive R Archive Network (CRAN) Shaun Wilkinson [aut, cre] GPL-3 2026-01-23 application/tgz https://CRAN.R-project.org/package=aphid doi:10.32614/CRAN.package.aphid