String Similarity Joins for Hamming and Levenshtein Distances

This project is a tool for words edit similarity joins (a.k.a. all-pairs similarity search) under small (< 3) edit distance constraints. It works for Levenshtein/Hamming distances and words from any alphabet. The software was originally developed for joining amino-acid/nucleotide sequences from Adaptive Immune Repertoires, where the number of words is relatively large (10^5-10^6) and the average length of words is relatively small (10-100).


Reference manual

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install.packages("RPatternJoin")

1.0.0 by Daniil Matveev, 2 years ago


Browse source code at https://github.com/cran/RPatternJoin


Authors: Daniil Matveev [aut, cre] , Martin Leitner-Ankerl [ctb, cph] , Gene Harvey [ctb, cph]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports Rcpp, stats

Suggests Matrix, testthat, stringdist

Linking to Rcpp, RcppArmadillo


See at CRAN