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>. It also includes a modified version of the Starcode all-pairs search algorithm (Zorita, Cuscó, and Filion 2015) <doi:10.1093/bioinformatics/btv053>.
| Version: | 0.4.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 0.12.18.3), RcppParallel (≥ 5.1.3), R6, S7 |
| LinkingTo: | Rcpp, RcppParallel |
| Suggests: | knitr, rmarkdown, pwalign, igraph, ggplot2 |
| Published: | 2026-06-03 |
| 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), Eduard Zorita [ctb] (Starcode algorithm and publication), Pol Cuscó [ctb] (Starcode algorithm and publication), Guillaume J. Filion [ctb] (Starcode algorithm and publication) |
| 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; see inst/licenses/span-lite-BSL-1.0-LICENSE. This package includes code from the 'ankerl' library owned by Martin Leitner-Ankerl under MIT License. This package includes a modified version of the Starcode all-pairs search algorithm described by Eduard Zorita, Pol Cuscó, and Guillaume J. Filion (2015). See inst/licenses/starcode-GPL-3-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, C++17 |
| Materials: | README, ChangeLog |
| CRAN checks: | seqtrie results |
| Reference manual: | seqtrie.html , seqtrie.pdf |
| Vignettes: |
seqtrie (source, R code) |
| Package source: | seqtrie_0.4.0.tar.gz |
| Windows binaries: | r-devel: seqtrie_0.4.0.zip, r-release: seqtrie_0.4.0.zip, r-oldrel: seqtrie_0.4.0.zip |
| macOS binaries: | r-release (arm64): seqtrie_0.4.0.tgz, r-oldrel (arm64): seqtrie_0.4.0.tgz, r-release (x86_64): seqtrie_0.4.0.tgz, r-oldrel (x86_64): seqtrie_0.3.5.tgz |
| Old sources: | seqtrie archive |
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