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 |