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 |
| Reference manual: | aphid.pdf |
| Vignettes: |
Introduction to the aphid package |
| 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 imports: | coil, debar, insect |
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