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seqtrie: Radix Tree and Trie-Based String Distances

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) <http://stevehanov.ca/blog/index.php?id=114>.

Version: 0.2.8
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: 2024-05-04
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

Documentation:

Reference manual: seqtrie.pdf
Vignettes: seqtrie

Downloads:

Package source: seqtrie_0.2.8.tar.gz
Windows binaries: r-devel: seqtrie_0.2.8.zip, r-release: seqtrie_0.2.8.zip, r-oldrel: seqtrie_0.2.8.zip
macOS binaries: r-release (arm64): seqtrie_0.2.8.tgz, r-oldrel (arm64): seqtrie_0.2.8.tgz, r-release (x86_64): seqtrie_0.2.8.tgz, r-oldrel (x86_64): seqtrie_0.2.8.tgz
Old sources: seqtrie archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=seqtrie to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.