A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>.
| Version: | 0.2.9 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 0.12.18.3), RcppParallel (≥ 5.1.3), R6, rlang, dplyr, stringi |
| LinkingTo: | Rcpp, RcppParallel, BH |
| Suggests: | knitr, rmarkdown, stringdist, qs, Biostrings, pwalign, igraph, ggplot2 |
| Published: | 2025-03-02 |
| DOI: | 10.32614/CRAN.package.seqtrie |
| Author: | Travers Ching [aut, cre, cph], Martin Moene [ctb, cph] (span-lite C++ library), Steve Hanov [ctb] (Trie levenshtein implementation in Python), Martin Leitner-Ankerl [ctb] (Ankerl unordered dense hashmap) |
| Maintainer: | Travers Ching <traversc at gmail.com> |
| BugReports: | https://github.com/traversc/seqtrie/issues |
| License: | GPL-3 |
| Copyright: | This package includes code from the 'span-lite' library owned by Martin Moene under Boost Software License 1.0. This package includes code from the 'ankerl' library owned by Martin Leitner-Ankerl under MIT License. This package contains data derived from Adaptive Biotechnologies "ImmuneCODE" dataset under Creative Commons Attribution 4.0. |
| URL: | https://github.com/traversc/seqtrie |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Materials: | README ChangeLog |
| CRAN checks: | seqtrie results |
| Reference manual: | seqtrie.pdf |
| Vignettes: |
seqtrie (source, R code) |
| Package source: | seqtrie_0.2.9.tar.gz |
| Windows binaries: | r-devel: seqtrie_0.2.9.zip, r-release: seqtrie_0.2.9.zip, r-oldrel: seqtrie_0.2.9.zip |
| macOS binaries: | r-devel (arm64): seqtrie_0.2.9.tgz, r-release (arm64): seqtrie_0.2.9.tgz, r-oldrel (arm64): seqtrie_0.2.9.tgz, r-devel (x86_64): seqtrie_0.2.9.tgz, r-release (x86_64): seqtrie_0.2.9.tgz, r-oldrel (x86_64): seqtrie_0.2.9.tgz |
| Old sources: | seqtrie archive |
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