kmeRs: K-Mers Similarity Score Matrix

Contains tools to calculate similarity score matrix for DNA k-mers. The pairwise similarity score is calculated using PAM or BLOSUM substitution matrix. The results are evaluated by similarity score calculated by Needleman-Wunsch (1970) <doi:10.1016/0022-2836(70)90057-4> global or Smith-Waterman (1981) <doi:10.1016/0022-2836(81)90087-5> local alignment. Higher similarity score indicates more similar sequences for BLOSUM and less similar sequences for PAM matrix; 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM and BLOSUM, respectively.

Version: 1.1.0
Depends: R (≥ 3.4.0)
Imports: tcR, rDNAse, utils, stats, Biostrings
Suggests: knitr, ape (≥ 4.0), rmarkdown
Published: 2018-11-03
Author: Rafal Urniaz ORCID iD [aut, cre]
Maintainer: Rafal Urniaz <rafal.urniaz at>
License: GPL-3
NeedsCompilation: no
Citation: kmeRs citation info
CRAN checks: kmeRs results


Reference manual: kmeRs.pdf
Vignettes: Introduction to the kmeRs R package
Package source: kmeRs_1.1.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: kmeRs_1.1.0.tgz, r-oldrel: kmeRs_1.1.0.tgz


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